Previous studies. washington. washington. ch>: > Hi Nathalie, > > It seems that CHARMM doesn't read the residue number correctly: > > 2011/6/29 Gianluca Interlandi <gianluca_at_u. washington. Gianluca On Thu, 6 Jan 2011, Gianluca Interlandi wrote: > Hi!One Bedroom Apartment, Sleeps 3 - £83 avg. washington. In reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. edu> wrote:Gianluca Interlandi. I'm > not sure whether the CHARMM program can read. Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. In reply to: Gianluca Interlandi: "Re: Changing Boundary conditions from PBC to non-periodic" Messages sorted by: [ attachment ] How would somebody want to simulate explicit water molecules without PBC? The water molecules will quickly diffuse and your protein be in vacuum. 6 ns/day for a 100k atom system with roughly those same parameters (and. 100% refund of amount payable if you cancel at least 14 days before check-in. uiuc. Biochemistry. washington. I doubt that there is a way to haveReply: Gianluca Interlandi: "Re: NAMD timestep and numsteps" Messages sorted by: [ attachment ] Hi NAMD users, I was running a simulation using NAMD with timestep 5 fs and numsteps 5000. edu> wrote:Next in thread: Gianluca Interlandi: "Re: Infiniband and PME gridsize" Reply: Gianluca Interlandi: "Re: Infiniband and PME gridsize" Messages sorted by: [ attachment ] I don't think we have ever run NAMD on infiniband. SASA in NAMD is used > internally to perform simulations in implicit solvent, whereas SASA in > VMD is used to analyse trajectories. edu) Date: Wed Jul 16 2014 - 00:32:49 CDT Next message: Sadegh Faramarzi Ganjabad: "Re:Subject: Re: Subject: Re:Re: New partial charges after patching" Previous message: Gianluca Interlandi: "Re: Force field design" Next in. > > Gianluca >Gianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. edu) Date: Wed Jun 15 2011 - 14:18:43 CDT Next message: Reichert, David: "RE: Question about equilibration" Previous message: Richard Wood: "Re: Question about equilibration" In reply to: Richard Wood: "Re: Question about. 10. >> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. Next in thread: Gianluca Interlandi: "Re: accuracy of measurement" Reply: Gianluca Interlandi: "Re: accuracy of measurement" Messages sorted by: [ attachment ] hi namd users. washington. edu) Date: Fri May 01 2009 - 12:18:05 CDT Next message: Grace Brannigan: "Re: crash with more than 96 processors (v2. VMD-L Mailing List. What are you trying to accomplish?Previous message: Gianluca Interlandi: "Re: SSD vs SSHD vs mechanical" In reply to: Gianluca Interlandi: "Re: SSD vs SSHD vs mechanical" Next in thread: Axel Kohlmeyer: "Re: SSD vs SSHD vs mechanical" Messages sorted by: [ attachment ] At present I don't think NAMD will let you write a jsLe mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit : > I am performing a simulation of a complex consisting of two proteins. Hemostasis in vertebrates involves both a cellular and a protein component. eduRe: Question about equilibration. Oktober 2013 07:12 > An: Roy Fernando > Cc: Axel Kohlmeyer; namd-l_at_ks. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. Reply: Gianluca Interlandi: "Re: Jarzinsky's equation" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] By having the force and the extension that the force is applied to you can> 2011/6/29 Gianluca Interlandi <gianluca_at_u. > > > > I have already run a bunch of pulling simulations in the NVE ensemble. Michel Espinoza-Fonseca: "Re: Vibrational. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build?On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi < gianluca_at_u. 7 with the PLUMED patch" Next in thread: Davide Branduardi: "Re: Compiling NAMD 2. From: Gianluca Interlandi (gianluca_at_u. Sunhwan On Jul 16, 2014, at 12:32 AM, Gianluca Interlandi <gianluca_at_u. > > I have already run a bunch of pulling simulations in the NVE ensemble. On the other hand, a 4 TB WD 7200RPM is under 200$. Oktober 2013 07:12 > An: Roy Fernando > Cc: Axel Kohlmeyer; namd-l_at_ks. Usually, this > is > written in the dcd file if you specified "DCDUnitCell yes" in your > NAMD > config file. 7 released" Messages sorted by: [ attachment ] Thank you very much! It seems to be up to 40% faster than the 2. washington. washington. a, three-dimensional structure of the complex between A1 and GpIbα used in this manuscript. 7b1 on NCSA Abe. From: Gianluca Interlandi <gianluca_at_u. In reply to: Gianluca Interlandi: "Re: namd ibverbs" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] This archive was generated by hypermail 2. at 298. Be the first to write a review. 1002/prot. 122076 s/step, which is 16% slower than using > the 6Re: Question about equilibration. com) Date: Sat Dec 04 2010 - 02:07:05 CST Next message: Gianluca Interlandi: "Re: Fwd: Installing NAMD on windows" Previous message: Gianluca Interlandi: "Re: Jarzinsky's equation" Next in thread: Gianluca Interlandi: "Re: Fwd:. 7b1 on NCSA Abe" Next in thread: Gianluca Interlandi: "Re: Namd-I: Implicit solvent problem" Messages sorted by: [ attachment ] Hi Enrico. 2016. edu) Date: Wed May 16 2007 - 14:43:41 CDT Next message: Ayşe Özlem Sezerman: "System charge" Previous message: Peter Freddolino: "Re: Minimization" In reply to: Viswanadham Sridhara: "How to unsubscribe ?" Messages. washington. Bathroom 1. washington. Here they are: a. com) Date: Sat Jul 04 2015 - 10:49:22 CDT Next message: Gianluca Interlandi: "multicore vs ibverbs" Previous message: Josh Vermaas: "Re: extra bonds" Maybe in reply to: Mitchell Gleed: "Re: replica exchange and GPU acceleration" Next in. edu) Date: Mon May 28 2007 - 10:33:29 CDT Next message: Gianluca Interlandi: "Re: Protein in/out of box" Previous message: Peter Freddolino: "Re: constraints on zinc ions" In reply to: Monika Sharma: "Protein in/out of box" Next in. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on small> 2011/6/29 Gianluca Interlandi <gianluca_at_u. washington. edu> > wrote: > are other people also using those GPUs? > > Previous message: Gianluca Interlandi: "Conversion for forces" In reply to: Gianluca Interlandi: "Conversion for forces" Next in thread: Gianluca Interlandi: "SMD and restart" Reply: Gianluca Interlandi: "SMD and restart" Messages sorted by: [ attachment ] This archive was generated by Research Assistant Professor gianluca@u. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. uiuc. The simulations were not performed at constant velocity > but at constant force. I was recording the energies once every 100 steps. I did what you and Gianluca suggested but still have two caveats. 0 and 2. From: Gianluca Interlandi (gianluca_at_u. 3 hours/ns (stepsize 1, fullElectFrequency 1 and stepspercycle 20). SASA in NAMD is used internally > to perform simulations in implicit solvent, whereas SASA in VMD is used to > analyse trajectories. Member since 2014. From: Gianluca Interlandi (gianluca_at_u. > > On Thu, Jul 12, 2012 at 3:21 PM, Gianluca Interlandi > <gianluca_at_u. washington. 7 with the PLUMED patch" Next in thread: Davide Branduardi: "Re: Compiling NAMD 2. edu> wrote: >> if you want to go low risk and don't have much experience with GPU, then >> probably the best deal you can currently get for running. RE: Force field design. Pavel Aprikian, # 1 Gianluca Interlandi, # 2 Brian A. Research Assistant Professor (Independent Lab) e-mail: gianluca@u. From: Gianluca Interlandi (gianluca_at_u. > > According to your banchmarks, it looks like the less expensive GTX285. Gianluca Interlandi, ‡, 1, 2 Olga Yakovenko, ‡, 1 An-Yue Tu,. SMD on center of mass. You should simulate it in explicit water (or try one of the implicitNext in thread: Gianluca Interlandi: "Re: accuracy of measurement" Reply: Gianluca Interlandi: "Re: accuracy of measurement" Messages sorted by: [ attachment ] hi namd users. }, author={Dagmara I. washington. Anderson: "Re: rlwrap problem on" In reply to: Frank Barry: "rlwrap problem on" Next in thread: Gianluca Interlandi: "Re: rlwrap problem on" Reply:. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). Gianluca, Looking at the code, it does not, but that would be easy to adapt from the NAMD's ComputeCrossterms. washington. VMD-L Mailing List. You should simulate it in explicit water (or try one of the implicitCompiling NAMD 2. edu> wrote:Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. 5923 Kcal/mol also we have 6. washington. washington. washington. > > > > Forget about creating a pdb file. edu> wrote: > Hi! > > Are there any benchmarks available which compare the performance of NAMD on > Lincoln (CUDA heterogenous cluster) with its performance on a traditional > CPU only cluster like Abe? >Re: editing the code of the non bonded pair potentials. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" Previous message: Gianluca Interlandi: "RE: DCD" In reply to: Gianluca Interlandi: "RE: DCD" Next in thread: Buddhadev Maiti: "RE: DCD"Re: Langevin damping coefficient. These are the lastIn reply to: Gianluca Interlandi: "Re: Vibrational mode analysis" Next in thread: Gianluca Interlandi: "Re: Vibrational mode analysis" Reply: Gianluca Interlandi: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] Hi Gianluca, Unfortunately I don't know from where you can get such tutorials. You simply load your trajectory > into VMDReply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] So your speed for 1 or 2 GPUs (based on what your sent) is about 1. washington. 7b4 is that> On Feb 8, 2007, at 11:49 PM, Gianluca Interlandi wrote: > > >I have a question concerning steered molecular dynamics simulations > >(constant force and constant velocity). From: Gianluca Interlandi (gianluca_at_u. My> On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. The other> Auftrag von Gianluca Interlandi > Gesendet: Sonntag, 27. edu) Date: Thu Apr 07 2011 - 16:55:51 CDT Next message: THANH NGUYEN: "SMD simulation: stop applying force during simulation?" Previous message: johan strumpfer: "Re: Abe versus Lincoln" In reply to: johan strumpfer: "Re:. Just source the Tcl file and use the 'unwrap' procedure. washington. edu) Date: Thu Feb 20 2014 - 13:15:51 CST Next message: zeynab mohamad hoseyni: "FATAL ERROR: EOF ENCOUNTERED READING CROSS-TERMS FROM PSF FILE" Previous message: Kenno Vanommeslaeghe: "Re: tools for Charmm" In reply to: Kenno Vanommeslaeghe: "Re:. There have been over 180 downloads and no complaints so far. Gianluca Interlandi 1 Affiliation 1 Department of Bioengineering, University of Washington, Seattle, Washington, USA. From: John Stone (johns_at_ks. View the profiles of professionals named "Gianluca Interlandi" on LinkedIn. MyFrom: Gianluca Interlandi (gianluca_at_u. In reply to: Gianluca Interlandi: "Re: Force field design" Next in thread: Axel Kohlmeyer: "Re: Force field design" Reply: Axel Kohlmeyer: "Re: Force field design" Messages sorted by: [ attachment ] On 24 July 2014 22:22, Gianluca Interlandi <gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. Location info. Reply: Gianluca Interlandi: "Re: query about wrapped coordinates" Messages sorted by: [ attachment ] Hi, Thanks again for your useful suggestions. On Tue, Jul 10, 2012 at 1:14 PM, Gianluca Interlandi < gianluca_at_u. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" From: Gianluca Interlandi (gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. In reply to: Gianluca Interlandi: "Re: Question about equilibration" Next in thread: Gianluca Interlandi: "Re: Question about equilibration" Reply: Gianluca Interlandi: "Re: Question about equilibration" Messages sorted by: [ attachment ] Because an X-ray is assumed to be a structure at "zero K" and an MD equilibrated. com) Date: Thu Apr 07 2011 - 14:21:33 CDT Next message: Gianluca Interlandi: "Re: Abe versus Lincoln" Previous message: Gianluca Interlandi: "Re: Abe versus Lincoln" In reply to: Gianluca Interlandi: "Re: Abe versus Lincoln" Next in thread: Gianluca Interlandi: "Re:. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). edu) Date: Thu Feb 20 2014 - 13:15:51 CST Next message: zeynab mohamad hoseyni: "FATAL ERROR: EOF ENCOUNTERED READING CROSS-TERMS FROM PSF FILE" Previous message: Kenno Vanommeslaeghe: "Re: tools for Charmm" In reply to: Kenno Vanommeslaeghe: "Re:. washington. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. 85. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. washington. From: Gianluca Interlandi (gianluca_at_u. washington. edu> Date: Monday, May 7, 2007 7:26 pm Subject: Re: namd-l: query about wrapped coordinates > I have actually found a much easier way of adding the crystal > information > to your trajectory. From: Gianluca Interlandi (gianluca_at_u. Bioengineering. Swett wrote: > From your email, it's apparent that you are in > the pharmacy school of the university of maryland. Entertainment. Re: Yet another NAMD speed concerns. 7 with the PLUMED patch" In reply to: Gianluca Interlandi: "Compiling NAMD 2. edu> wrote: > Hi Fatemeh, > > Thanks for replying. Gianluca On Thu, 6 Jan 2011, Gianluca Interlandi wrote: > Hi! Next in thread: Gianluca Interlandi: "Scale" Messages sorted by: [ attachment ] Gianluca: Using VMD with the attached script should solve that. washington. Eddie: "gentoo ebuild" Previous message: Robert Johnson: "Re: ABF/Steered MD for DNA Hybridization on Carbon Nanotubes" Maybe in reply to: Norman Geist: "AW: AW: Running NAMD on Forge (CUDA)" Complex between VWF A1 and GpIbα and amino acid sequence of the A1 domain. From: Gianluca Interlandi (gianluca_at_u. What can be the possible cause for this or does it happens naturallyOn Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. uiuc. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" Previous message: Gianluca Interlandi: "RE: DCD" In reply to: Gianluca Interlandi: "RE: DCD" Next in thread: Buddhadev Maiti: "RE: DCD"Gianluca Interlandi Foege N430E gianluca_at_uw_dot_edu. You simply load your trajectory > > into VMD On 7/7/2011 6:08 PM, Gianluca Interlandi wrote: > Francesco, > > Just a hint. Gianluca Interlandi, research assistant professor, and Wendy Thomas, professor: Antibody Dependent Enhancement, a type of immune system backfiring that causes increased infection in cells, is likely responsible for disappointing results on experimental vaccines for SARS and MERS, and. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. I would be > happy if somebody could point me out to some scripts which help me performOn Thu, 5 Apr 2012, Gianluca Interlandi wrote: > What is the advantage of the multicore version of charm++ versus net-linux? > Is multicore faster if I'm running for example on a 32-core magny-Cours AMDFrom: Gianluca Interlandi (gianluca_at_u. From: Mitchell Gleed (aliigleed16_at_gmail. In reply to: Gianluca Interlandi: "Conversion for forces" Messages sorted by: [ attachment ] Gianluca, kcal/mol is an energy so kcal/mol/A should be a force kcal/mol/A^2 is probably a force constant for a spring. Eddie: "gentoo ebuild" Previous message: Robert Johnson: "Re: ABF/Steered MD for DNA Hybridization on Carbon Nanotubes" Maybe in reply to: Norman Geist: "AW: AW: Running NAMD on Forge (CUDA)"Gianluca Interlandi, ‡, 1, 2 Olga Yakovenko, ‡, 1 An-Yue Tu,. From: Victor (ovchinnv_at_gmx. Re: How to unsubscribe ? From: Gianluca Interlandi (gianluca_at_u. washington. From: Gianluca Interlandi (gianluca_at_u. phone: 206 685 4435; office: N430E Foege Hall (Bioengineering) homepage: New UW Bioengineering research assistant professor Gianluca Interlandi studies the molecular function of blood proteins involved in hemostasis and clotting. > On Thu, Dec 2, 2010 at 2:35 PM, Gianluca Interlandi <gianluca_at_u. Re: Langevin process in NAMD tutorial" Previous message: Basak Isin: "Re: Regarding answering questions in a forum. It's > slightly faster but still not that much faster than running on 16 CPU cores. com) Date: Thu Apr 05 2012 - 16:21:19 CDT Next message: Axel Kohlmeyer: "Re: DCD" Previous message: Buddhadev Maiti: "RE: DCD" In reply to: Gianluca Interlandi: "Re: DCD" Messages sorted by: [ attachment ] Hi Maiti, In TCL you can also use the 'animate' command. uiuc. It's > slightly faster but still not that much faster than running on 16 CPU cores. Chemistry. washington. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? On Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. From: Gianluca Interlandi (gianluca_at_u. Bathrooms: 1. Just a good MD toy ! Victor owner-namd-l_at_ks. washington. We are building a smaller cluster though in the lab and will test the scalability2006/9/6, Gianluca Interlandi <gianluca_at_u. Reply: Gianluca Interlandi: "Re: Abe versus Lincoln" Messages sorted by: [ attachment ] Hi Gianluca, Using 4 Lincoln nodes with a 112580 atoms system I get 9. The otherGianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. 15 K 1 KT = 2. In reply to: Gianluca Interlandi: "Vibrational mode analysis" Next in thread: Richard Law: "Re: Vibrational mode analysis" Messages sorted by: [ attachment ] CHARMM does normal mode. washington. washington. 6 : Tue Dec 27 2016 - 23:21:14 CST Gianluca Interlandi's 67 research works with 730 citations and 2,578 reads, including: Rate limiting step of the allosteric activation of the bacterial adhesin FimH investigated by molecular. From: Buddhadev Maiti (bmaiti_at_gsu. washington. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. washington. Balcony. edu) Date: Mon May 28 2007 - 10:33:29 CDT Next message: Gianluca Interlandi: "Re: Protein in/out of box" Previous message: Peter Freddolino: "Re: constraints on zinc ions" In reply to: Monika Sharma: "Protein in/out of box" Next in. Gianluca > Gianluca > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build? I wonder if the prebuilt > smp one is just not > working for you. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallmargin errors. 7 out the door on Friday. From: Gianluca Interlandi (gianluca_at_u. GianlucaHosted by Gianluca Interlandi. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). It's > slightly faster but still not that much faster than running on 16 CPU cores. washington. washington. Does Berendsen increase viscosity of water? From: Gianluca Interlandi (gianluca_at_u. Gianluca On Thu, 6 Jan 2011, Gianluca Interlandi wrote: > Hi!In reply to: Gianluca Interlandi: "Re: Question about equilibration" Next in thread: Gianluca Interlandi: "Re: Question about equilibration" Reply: Gianluca Interlandi: "Re: Question about equilibration" Messages sorted by: [ attachment ] Because an X-ray is assumed to be a structure at "zero K" and an MD equilibrated. VMD-L Mailing List. Try copying it again from where the simulation was run. Best, Jerome Le mardi 3 octobre 2006 01:01, Gianluca Interlandi a écrit : > Auftrag von Gianluca Interlandi > Gesendet: Sonntag, 27. edu> wrote: >>> if you want to go low risk and don't have much experience with GPU, then >>> probably the best deal you can currently get for running NAMD on smallYesterday at about 11:45 a. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. The difference is usually after the > 4th decimal after the period. From: Gianluca Interlandi (gianluca_at_u. Michel Espinoza-Fonseca: "Re: Vibrational mode analysis" In reply to: L. I was getting 2. edu] Sent: Thursday, April 05, 2012 5:04 PM To: Buddhadev Maiti Cc: Jérôme Hénin; namd-l_at_ks. > > Gianluca > > On Wed, 23 Sep 2015, John Stone. On Thu, Jul 12, 2012 at 3:53 PM, Gianluca Interlandi < gianluca_at_u. Gianluca On Mon, 11 Apr 2011, Axel Kohlmeyer wrote: > On Mon, Apr 11, 2011 at 3:41 PM, Gianluca Interlandi > <gianluca_at_u. washington. I doubt that there is a way to have NAMD output theReply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] have you tried the multicore build? I wonder if the prebuilt smp one is just not working for you. Re: Help building a desktop for namd. From: Gianluca Interlandi (gianluca_at_u. edu) Date: Thu Apr 30 2009 - 12:15:37 CDT Next message: bo liu: "Re: Optimizing configuration option for fast calculations" Previous message: Jerome Henin: "Re: Benzene PSF" In reply to: Peter Freddolino: "Re: NAMD 2. 7 out the door on Friday. > > Forget about creating a pdb file. Gianluca Interlandi 1 Affiliation 1 Department of Bioengineering, University of Washington, Seattle, Washington, USA. washington. The energy term mustOn Mon, 11 Apr 2011, Gianluca Interlandi wrote: > Salvador, > > You might also want to apply for computing time at one of the national > supercomputing centers through Teragrid. Gianluca On Thu, 20 Feb 2014, Kenno Vanommeslaeghe wrote: > I likely don't know the answer to this, but just to clarify the question, you > are talking about an Xplor topology and/or parameter (not psf) file you want > to convert to a CHARMM topology and/or parameter file, right? > > On 02/20/2014 03:31 AM, Peter Reinke wrote: >> Dear all, >>Gianluca, Looking at the code, it does not, but that would be easy to adapt from the NAMD's ComputeCrossterms. Managing Member/Principal Atlantic Mortgage Partners, LLC Jun 2009 - Jun 2012 3 years 1. edu on behalf of Gianluca Interlandi [gianluca_at_u. > On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi <gianluca_at_u. > > gianluca, >Next in thread: Gianluca Interlandi: "Re: Help building a desktop for namd" Messages sorted by: [ attachment ] On Mon, Apr 11, 2011 at 5:21 PM, Gianluca Interlandi <gianluca_at_u. Hope the video helps, but now I'm embarrassed. washington. 7b1)" Previous message: Christopher Hartshorn: "Re: FEP tutorial graph question" In reply to: Peter Freddolino: "Re: NAMD 2. From: Gianluca Interlandi (gianluca_at_u. 7 released" In reply to: Jim Phillips: "Re: NAMD 2. Previous message: Gianluca Interlandi: "Re: tools for Charmm" In reply to: Gianluca Interlandi: "Re: Charmm" Messages sorted by: [ attachment ] On 02/20/2014 01:10 PM, Gianluca Interlandi wrote: > I usually use the CHARMM program itself to generate a CHARMM PSF file. washington. edu> wrote: >> blades generally tend to be a bit slower than "normal" nodes. edu) Date: Thu Apr 05 2012 - 16:30:29 CDT Next message: Gianluca Interlandi: "RE: DCD" Previous message: Axel Kohlmeyer: "Re: DCD" In reply to: Buddhadev Maiti: "RE: DCD" Next in thread: Gianluca Interlandi: "RE: DCD" Reply: Gianluca Interlandi: "RE: DCD". edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" From: Gianluca Interlandi (gianluca_at_u. Display options. It's > slightly faster but still not that much faster than running on 16 CPU cores. washington. NAMD supports CHARMM22 parameter files. > > Gianluca > > > On Thu, 12 Jul 2012, Aron Broom wrote: > > have you tried the multicore build?Next in thread: Gianluca Interlandi: "Re: NAMD 2. unam. Mechanism of allosteric propagation across a β-sheet structure investigated by molecular dynamics simulations. 7b1 - effects of configuration parameters and hardware. From: Gianluca Interlandi (gianluca_at_u. The read speed of the trajectory will go much faster if you select the "load all at once" checkbox in the moleculeRe: Vibrational mode analysis. edu> wrote: >> blades generally tend to be a bit slower than "normal" nodes. washington. > > Any ideas how it affects the stability of a simulated protein? If On Thu, Jul 12, 2012 at 4:58 PM, Gianluca Interlandi < gianluca_at_u. com) Date: Wed Sep 18 2013 - 14:48:11 CDT Next message: Gianluca Interlandi: "Re: Open VMD from a remote host" Previous message: John Stone: "Re: Open VMD from a remote host" In reply to: Gianluca Interlandi: "Open VMD from a remote host" Next in thread: Gianluca. 7 released" Reply: Gianluca Interlandi: "Re: NAMD 2. You simply load your trajectory > into VMD Reply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] So your speed for 1 or 2 GPUs (based on what your sent) is about 1. edu) Date: Fri May 01 2009 - 12:18:05 CDT Next message: Grace Brannigan: "Re: crash with more than 96 processors (v2. I needed to install the 'patch' program. Next in thread: Gianluca Interlandi: "Re: Namd-I: Implicit solvent problem" Messages sorted by: [ attachment ] Hi Enrico. Kitchen. edu> wrote: > Dear all, > > Does anybody have any recommendation how to convert a solvated system > (protein + solvent + ions) PDB + PSF from the CHARMM to the Amber force > field so that it can be used in NAMD with the. Reply: Gianluca Interlandi: "Re: Regarding thermostats" Reply: Marcos Sotomayor: "Re: Regarding thermostats" Messages sorted by: [ attachment ] Dear NAMD users, Lately in the lab we have been discussing about which thermostat use in our simulations. Spaces. I would be > happy if somebody could point me out to some scripts which help me perform(no subject) From: BIPLAB NANDI (dafodils2002_at_gmail. The Bacterial Fimbrial Tip Acts as a Mechanical Force Sensor. > On Fri, 9 Feb 2007, Gianluca Interlandi wrote: > > > Dear Marcos, > > > > Thanks a lot for your answer and for offering me your help. 7 with the PLUMED patch" In reply to: Gianluca Interlandi: "Compiling NAMD 2. MyOn Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi < gianluca_at_u. UW Bioengineering announces that Barry Lutz is hired as tenure-track faculty, Gianluca Interlandi joins faculty and Suzie Pun is promoted to full professorIn reply to: Gianluca Interlandi: "NAMD + nice" Messages sorted by: [ attachment ] Nice (process priority) is only supported in NET version of Charm++. washington. AMBER does, and so does GROMACS. washington. I wanted to briefly update here on my > experience. washington. > On Wed, Dec 1, 2010 at 1:54 AM, Gianluca Interlandi <gianluca_at_u. I know the lack of treatment of the hydrophobic part but the point In reply to: Gianluca Interlandi: "Conversion for forces" Messages sorted by: [ attachment ] Gianluca, kcal/mol is an energy so kcal/mol/A should be a force kcal/mol/A^2 is probably a force constant for a spring. edu) Date: Thu Apr 05 2012 - 17:04:15 CDT Next message: Gianluca Interlandi: "multicore versus net-linux" Previous message: Gianluca Interlandi: "RE: DCD" In reply to: Gianluca Interlandi: "RE: DCD" Next in thread: Buddhadev Maiti: "RE: DCD"UW Bioengineering is pleased to announce the hires of faculty Barry Lutz and Gianluca Interlandi, as well as the promotion of Suzie Pun to full professor. PMID: 37700555; DOI: 10. 1002/prot. edu) Date: Thu Jun 15 2006 - 21:01:04 CDT Next message: Taeho Kim: "free energy calculate" From: Gianluca Interlandi (gianluca_at_u. In the text field you can enter your atom selection, e. I > > attach a plot of a constant velocity simulation where I'm pulling two > > proteins apart. g. edu Search for more papers by this author> On Thu, Dec 2, 2010 at 2:35 PM, Gianluca Interlandi <gianluca_at_u. washington. Gianluca Interlandi Foege N430E gianluca_at_uw_dot_edu My laboratory combines tools from computational structural biology, like molecular dynamics simulations and Monte Carlo methods, with biochemical and biophysical assays to unravel the molecular basis behind biological processes like the blood coagulation cascade and cellular adhesion. edu> > wrote: > Roy, > > I think that you are confusing two things. PMID: 37700555; DOI: 10. In this way, you could get a feeling what NAMD can do before you > invest money. From: Gianluca Interlandi (gianluca_at_u. edu) Date: Thu Jun 15 2006 - 21:01:04 CDT Next message: Taeho Kim: "free energy calculate" Previous message: L. washington. edu> wrote: > Hi Fatemeh, > > Thanks for replying. Interlandi G. edu> wrote: > Dear all, > > Does anybody have any recommendation how to convert a solvated system > (protein + solvent + ions) PDB + PSF from the CHARMM to the Amber force > field so that it can be used in NAMD with the Abmer force field > parameters? > > Thanks, > Maybe in reply to: Gianluca Interlandi: "Re: query about wrapped coordinates" Next in thread: Gianluca Interlandi: "Re: query about wrapped coordinates" Reply: Gianluca Interlandi: "Re: query about wrapped coordinates" Messages sorted by: [ attachment ] Hi, Thanks again for your useful suggestions. 7b1 on Abe" Previous message: Gianluca Interlandi: "Re: Yet another NAMD speed concerns" In reply to: Gianluca Interlandi: "Re: Yet another. GianlucaFrom: Gianluca Interlandi (gianluca_at_u. > You could build a PC with the Asus p5Q Pro Motherboard, Intel Quadcore Q8200 > and two GTX 285 cards for under 900$ (plus the cost of the usual PC > components). washington. org/0000-0001-5445-9587; Department of Bioengineering, University of Washington, Seattle, Washington. edu> wrote: > A few of the simulations aborted with the following message: >> "ERROR: Atoms moving too fast; simulation has become unstable. In the NAMD folder that you downloaded there >> is a file called "notes. edu> wrote: > I would like to calculate the free energy of a protein-protein complex using > the Jarzinsky's equation from already performed SMD simulations. Just a good MD toy ! Victor owner-namd-l_at_ks. washington. Re: Yet another NAMD speed concerns. > However, topology and parameters for water and ions are. Next in thread: Gianluca Interlandi: "Re: NAMD 2. edu) Date: Fri Jul 13 2012 - 14:08:57 CDT Next message: Dr. Re: Vibrational mode analysis. Facebook gives people the power to share and makes the world more open and connected. Cancellation policy. washington. edu> wrote: > With multicore I get 96 sec per 1000 steps from the Benchmark time. C; the more troublesome part is the lack of long-range electrostatic treatments. Maybe the file was not transferred correctly to your desktop PC. edu Subject: RE: vmd-l: Can't read DCD files generated using NAMD. From: Gianluca Interlandi [gianluca_at_u. There are 3 professionals named "Gianluca Interlandi", who use LinkedIn to exchange. The only significant change since 2. Living Room. You should simulate it in explicit water (or try one of the implicit From: Gianluca Interlandi <gianluca_at_u. Reply: Gianluca Interlandi: "Re: Running NAMD on Forge (CUDA)" Messages sorted by: [ attachment ] have you tried the multicore build? I wonder if the prebuilt smp one is just not working for you. E-mail: [email protected],. , the force on the SMD atom gets huge. Whitfield, 2 Esther Bullitt, 4 Ronald E. Kisiela, # 1 , * Hovhannes Avagyan, # 1 Della Friend, 2 Aachal Jalan, 1 Shivani Gupta, 3 Gianluca Interlandi, 3 Yan Liu, 4 Veronika Tchesnokova, 1 Victoria. washington. Eric Klavins Professor. Research Assistant Professor [email protected]> > wrote:VMD-L Mailing List. , "not. Next in thread: Gianluca Interlandi: "Re: Help building a desktop for namd" Messages sorted by: [ attachment ] On Mon, Apr 11, 2011 at 5:21 PM, Gianluca Interlandi <gianluca_at_u. SASA in NAMD is used > internally to perform simulations in implicit solvent, whereas SASA in > VMD is used to analyse trajectories. washington. washington. Name : Current Position : Tim Connolley, Bioengineering 2005 : Michigan State Mechanical Engineering Graduate Program: Brett Anderson, Bioengineering 2006Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of HealthCorrespondence to: Gianluca Interlandi, Department of Bioengineering, University of Washington Box 355061, 3720 15th Ave NE, Seattle, WA 98195-5061, USA. washington. edu) Date: Tue Jul 15 2014 - 22:32:35 CDT Next message: Gianluca Interlandi: "RE: Force field design" Previous message: Aron Broom: "Re: Force field design" In reply to: Abhishek TYAGI: "Force field design" Next in thread: Mayne,. From: Gianluca Interlandi (gianluca_at_u. Rachel Tsai 1 , Gianluca Interlandi 1 Affiliation 1 Department of Bioengineering, University of Washington, Seattle, Washington, USA. washington. uiuc. edu Search for more. > 2011/6/29 Gianluca Interlandi <gianluca_at_u. edu> wrote: > Roy, > > I think that you are confusing two things. Neil King Assistant Professor. (Oct-Nov 1997) Spanish: Fluent written and spoken German: Basic Knowledge WORK EXPERIENCE 2019 October: Founder Host. Citat Gianluca Interlandi <gianluca_at_bioc. From: Gianluca Interlandi [gianluca_at_u. Cheers, Johan On Thu, Apr 7, 2011 at 4:40 PM, Gianluca Interlandi> 2011/6/29 Gianluca Interlandi <gianluca_at_u. The more tasks you have the > more frequently the CPUs need to update each other about the position > of Next message: Gianluca Interlandi: "Re: Fwd: Installing NAMD on windows" Previous message: Gianluca Interlandi: "Re: Jarzinsky's equation" Next in thread: Gianluca Interlandi: "Re: Fwd: Installing NAMD on windows" Reply: Gianluca Interlandi: "Re: Fwd: Installing NAMD on windows" Reply: Axel Kohlmeyer: "Re: Fwd: Installing NAMD on windows" Gianluca On Thu, 12 Jul 2012, Aron Broom wrote: > have you tried the multicore build? I wonder if the prebuilt smp one is just not > working for you. 50% refund of amount payable if you cancel at least 7 days before check-in. edu on behalf of Gianluca Interlandi [gianluca_at_u. washington. washington. Eric Klavins Professor. washington. Is it still possible to apply Jarzinsky's equation? > Also, according to your publication I have to integrate the work done along the. edu) Date: Mon Apr 11 2011 - 16:21:27 CDT Next message: Gianluca Interlandi: "Re: Help building a desktop for namd" Previous message: Axel Kohlmeyer: "Re: Help building a desktop for namd" In reply to: Axel Kohlmeyer: "Re:. edu) Date: Thu Jul 16 2015 - 16:20:34 CDT Next message: Simon Kit Sang Chu: "Minimization without MD" Previous message: Gianluca Interlandi: "Re: namd ibverbs" In reply to: Gianluca Interlandi: "Re: namd ibverbs" Next in thread: Maxime Boissonneault: "Re: namd ibverbs" The bacterial adhesin FimH is a model for the study of protein allostery because its structure has been resolved in multiple configurations, including the active and the inactive state. > On Wed, 16 Sep 2020 at 11:40, Gianluca Interlandi <gianluca_at_u. ch +41 (0) 1 635 55 93SMD on center of mass. > Le 2015-07-16 17:20, Gianluca Interlandi a écrit : >> Also, apropos documentation. Previous message: Gianluca Interlandi: "Re: Compiling NAMD 2. edu> > I suspect that E3_19 might not be stable with this type of implicit solvent > model (it doesn't contain a term to take the non-polar solvation energy into > accout). I would be > happy if somebody could point me out to some scripts which help me performDCD. washington. edu > Subject: Re: namd-l: DCD > > Load your psf+dcd into VMD. edu> > wrote:Re: Help building a desktop for namd. On Tue, 14 Dec 2004, Gianluca Interlandi wrote: > Dear NAMD users, > > I have two independent questions: > > 1) Are there any experiences about the scalability running NAMD on > infiniband? I have been running NAMD on myrinet and, as an example, for > a system with 51000 atoms I get a seedup of 14 on 16 CPUs (dual opteron > 1800+). edu) Date: Thu Apr 09 2015 - 17:39:49 CDT Next message: Gianluca Interlandi: "Re: measure sasa not consistent" Previous message: John Stone: "Re: measure sasa not consistent" Next in thread: Gianluca Interlandi: "Re: measure energy"> From: Gianluca Interlandi [gianluca_at_u. edu: "Re: high (or low) pressure readings" Next in thread: Gianluca Interlandi: "Infiniband and PME gridsize" Reply: Gianluca Interlandi: "Infiniband and PME gridsize" Reply: Brian Bennion: "Re: fatal error"> On Tue, Aug 7, 2012 at 4:16 PM, Gianluca Interlandi <gianluca_at_u. FimH. Previous message: Gianluca Interlandi: "NAMD 2. at 298. prm". Rachel Klevit WRF Endowed Chair in Biochemistry. edu) Date: Sat Apr 25 2009 - 12:05:17 CDT Next message: Gianluca Interlandi: "NAMD 2.