[gmx-users] different results when using different number cpus

Dear all, 　　I used Gromacs3.3.1 to do a simulation about two proteins in water(tip3p). I run two similar simulations, one for 2 cpus, while the other for 16 cpus. The two simulations have the same .gro, .top, and the same .mdp files. I found the results were not the same. In the 2 cpus

Re: [gmx-users] Gromacs on IBM cluster

Dear GMX users, I would like to give some feedback about my experience regarding the compilation of Gromacs 3.3.1 on the IBM cluster using the IBM compilers. Since I was unable to test a compilation with gcc, because gcc is not instaled, I've decided to recompile Gromacs with the IBM compilers

Re: [gmx-users] different results when using different number cpus

Hi, With Gromacs and (nearly) all other MD packages you will never be able to get binary identical results when running on different number of CPUs. Since MD is chaotic, the results can be very different. Berk. From: Carsten Kutzner [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS

[gmx-users] different results when using different number cpus

Message: 4 Date: Wed, 05 Dec 2007 14:19:28 +0100 From: Berk Hess [EMAIL PROTECTED] Subject: Re: [gmx-users] different results when using different number cpus To: gmx-users@gromacs.org Message-ID: [EMAIL PROTECTED] Content-Type: text/plain; format=flowed Hi, With Gromacs and (nearly)

[gmx-users] Re: fullerene topology

I forgot to ask if there is a forcefield for gromacs that will handle fullerenes. Is there? -Adam On Dec 5, 2007 1:17 PM, Adam Fraser [EMAIL PROTECTED] wrote: I'm trying to either build or find topology files for buckminster fullerene (C60). Does anyone know where I could find such files?

[gmx-users] Ambconv running

Hi, I am trying to use AMBCONV. However, it gives me a segmentation fault when I try to run it. I have seen that other users have posted a similar problem with the program on the mailing list. It seems to me that AMBCONV only uses older Amber formats. I have even generated that using set

[gmx-users] fullerene topology

I'm trying to either build or find topology files for buckminster fullerene (C60). Does anyone know where I could find such files? If not, does anyone know of literature that would help me build C60? I already have a pdb of the structure... I just need accurate partial charges to build the

RE: [gmx-users] fullerene topology

Have you looked at the information / forcefields for carbon nanotubes? Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524

Re: [gmx-users] different results when using different number cpus

Hi Dechang, it is normal that results are not binary identical if you compare the same MD system on different numbers of processors. If you use PME then you will probably get slightly different charge grids for 2 and for 16 processors - since the charge grid has to be divisible by the number of

[gmx-users] Scaling Coulomb interactions with lambda, on a pair-wise basis

Hi, I am looking to scale non-bonded interactions between two atoms with the lambda parameter, while keeping other interactions unchanged. I am not sure how to do this for Coulomb interactions. Scaling the Lennard-Jones interactions between a specific atom pair seems straightforward, by

Re: [gmx-users] Ambconv running

you shall use AMBER's new2oldparm new old to get the old format file. I remember that David Mobley has another ambconv script on his website (http://www.alchemistry.org/) but it is not accessible right now. Regards, Yang Ye On 12/6/2007 3:52 AM, Shozeb Haider wrote: Hi, I am trying to

Re: [gmx-users] different results when using different number cpus

1. how long is the simulation? 2. did you start from equilibration (with gen_vel=yes) or production md? 3. ... On 12/5/2007 8:28 PM, Dechang Li wrote: Dear all, 　　I used Gromacs3.3.1 to do a simulation about two proteins in water(tip3p). I run two similar simulations, one for 2 cpus,

Re: [gmx-users] Replica Exchange MD using Gromacs

Thank you very much all for your consideration and fruitful advices. Regards, Monika On Wed, 2007-12-05 at 18:15 +1100, Mark Abraham wrote: Xavier Periole wrote: Dear Monika, the setup of a REMD simulation is actually quite straightforward. In the following I describe steps that

[gmx-users] Re: gmx-users Digest, Vol 44, Issue 14

Hi, Mark You mean I should use gcc to compile the fftw, or both of fftw and gromacs? In fact I want to install a parellel gromacs, so perhaps I can install fftw with gcc, and install gromacs with xlc and mpcc? Thanks for your response. Li Zhenhai Department of Engineering

Re: [gmx-users] different results when using different number cpus

Yang Ye wrote: 1. how long is the simulation? 2. did you start from equilibration (with gen_vel=yes) or production md? 3. ... On 12/5/2007 8:28 PM, Dechang Li wrote: Dear all, 　　I used Gromacs3.3.1 to do a simulation about two proteins in water(tip3p). I run two similar