[gmx-users] Gromacs 3.3.1. and 3.3.3

Hi Users, I have run protein system till 25ns in gromacs version 3.3.1 in dual processor system. Now I want to run new systems in cluster with gromacs version 3.3.3, in two cases the protein system is same but difference in few residues, If run new system in cluster compare the results with

[gmx-users] how to use gromacs for steered molecular dynamics(SMD)

Hi, gmx-users i want to use gromacs to pull a small ligand through a protein channel and study the interaction between the ligand and the protein during this process. However, i have not found out any useful information about steered molecular dynamics(SMD) using Gromacs software. What are the di

[gmx-users] editconf subroutine

Hello, I how does editconf subroutine calculate the triclinc box dimensions (v1(x), v2(y), v3(z), v1(y) etc) from, for example, a .pdf file that has lattice dimensions information (a, b, c, alpha, beta, gamma). I would really appreciate a mathematical formula for each of these elements (v1(x), v2(

[gmx-users] Problems installing GMX 4.0 RC4

Hi, I've been working to install the latest release candidate from Gromacs 4.0; I have installed RC1 and RC2 without any problems on our cluster. We are running Mac OSX 10.3.9 on PowerPC nodes (G5 processors). My installation process for installing mdrun is really pretty textbook: ./confi

Re: [gmx-users] Charge groups, PME and ions [SOLVED]

David van der Spoel wrote: Andreas Kring wrote: Hello all. I have read the manual and searched the archives, but I am still a little confused so here goes: I am going to perform an MD simulation of a molecule consisting of 38 atoms and with a total charge of -4e (water as the solvent). For

[gmx-users] Final (?) release candidate (4) before Gromacs-4.0

Hi, I think we have fixed all issues with the release candidates, and I have just put the rc4 version at ftp://ftp.gromacs.org/pub/beta/gromacs-4.0_rc4.tar.gz Please test this to check whether there are any showstopper bugs :-) Although I'm sure there are still some minor issues, our curre

Re: [gmx-users] GROMACS performance on 10 GBit/s or 20Gbit/s infiniband

Hi, On Oct 6, 2008, at 6:46 AM, Himanshu Khandelia wrote: We are buying a new cluster with 8-code nodes and infiniband, and have a choice between 10 Gbit/s and 20 Gbit/s transfer rates between nodes. I do not immediately see the need for 20GBit/s between nodes, but thought it might be wor

Re: [gmx-users] Charge groups, PME and ions

Andreas Kring wrote: Hello all. I have read the manual and searched the archives, but I am still a little confused so here goes: I am going to perform an MD simulation of a molecule consisting of 38 atoms and with a total charge of -4e (water as the solvent). For this molecule it is not pos

Re: [gmx-users] g_rmsf over time windows

Hi Tsjerk Whether that's enough is largely dependent on the size of your protein You should check whether you went beyond relaxation by inspecting the cosine content of the first few eigenvectors. This by itself does not mean anything. If it levels off at 0.1 nm, okay, that's pretty good, but t

[gmx-users] gromacs 4-rc2 and parallel tempering

Dear Gromacs Users and Developers, I tried to perform a parallel tempering simulation with gromacs 4 rc2, using two replica. I think that the way of doing so is the same of gromacs 3, but it doesn't work I have two topol.tpr file: topol0.tpr and topol1.tpr and I run gromacs as: mpirun -np 2

Re: [gmx-users] Binary compatibility Gromacs 3.x <-> 4.0

On Wed, 2008-10-08 at 17:33 +0200, David van der Spoel wrote: > >>> Explanation: I am working on a package of Gromacs 4 that is going > to be > >>> included in Fedora. Is there still a need to have a separate package for > >>> Gromacs 3.3.x or is just Gromacs 4 enough? > >> Gromacs 4.0 can read all

RE: [gmx-users] Binary compatibility Gromacs 3.x <-> 4.0

Hi, The latest version is not officially out though. We expect the official release very soon. When do you need it? Berk > Subject: Re: [gmx-users] Binary compatibility Gromacs 3.x <-> 4.0 > From: [EMAIL PROTECTED] > To: gmx-users@gromacs.org > Date: Wed, 8 Oct 2008 18:30:03 +0300 > > On Wed,

[gmx-users] Charge groups, PME and ions

Hello all. I have read the manual and searched the archives, but I am still a little confused so here goes: I am going to perform an MD simulation of a molecule consisting of 38 atoms and with a total charge of -4e (water as the solvent). For this molecule it is not possible to make charge g

Re: [gmx-users] Binary compatibility Gromacs 3.x <-> 4.0

Jussi Lehtola wrote: On Wed, 2008-10-08 at 17:27 +0200, David van der Spoel wrote: Jussi Lehtola wrote: Hi, are GROMACS 4.0 files binary compatible with GROMACS 3.(3.)x files? Explanation: I am working on a package of Gromacs 4 that is going to be included in Fedora. Is there still a need to

Re: [gmx-users] Binary compatibility Gromacs 3.x <-> 4.0

On Wed, 2008-10-08 at 17:27 +0200, David van der Spoel wrote: > Jussi Lehtola wrote: > > Hi, > > > > > > are GROMACS 4.0 files binary compatible with GROMACS 3.(3.)x files? > > > > Explanation: I am working on a package of Gromacs 4 that is going to be > > included in Fedora. Is there still a ne

Re: [gmx-users] Binary compatibility Gromacs 3.x <-> 4.0

Jussi Lehtola wrote: Hi, are GROMACS 4.0 files binary compatible with GROMACS 3.(3.)x files? Explanation: I am working on a package of Gromacs 4 that is going to be included in Fedora. Is there still a need to have a separate package for Gromacs 3.3.x or is just Gromacs 4 enough? Gromacs 4.0

[gmx-users] Binary compatibility Gromacs 3.x <-> 4.0

Hi, are GROMACS 4.0 files binary compatible with GROMACS 3.(3.)x files? Explanation: I am working on a package of Gromacs 4 that is going to be included in Fedora. Is there still a need to have a separate package for Gromacs 3.3.x or is just Gromacs 4 enough? --

[gmx-users] Re: I am not able to write the cyclohexane topology files

gurgo> Jinyao Wang wrote: >> Hi, >> I want to carry out cyclohexane simulation with OPLS-AA. However, I am not >> able to write the cyclohexane topology >> files. If someone could sent me a cyclohexane OPLS-AA topology I'd very much >> appreciate it. Use this, thank Jochen Hub. http://www.mail-

Re: [gmx-users] g_rmsf over time windows

Hi Giordano, > I agree that 10 ns > are a short sampling but the total simulation time is 15 ns + 2 ns I > used to reach 298K; Whether that's enough is largely dependent on the size of your protein You should check whether you went beyond relaxation by inspecting the cosine content of the first f

Re: [gmx-users] g_rmsf over time windows

Hi Tsjerk, thanks for your reply. I have inspected a trajectory movie with vmd and made a superimposition of the starting and last configuration with the reference structure (which is just the the crystallographic pdb) and (inspecting them visually), I do not see any significant conformational ch

Re: [gmx-users] g_rmsf over time windows

Hi Giordano, Do you have a conformational change? If you consider unidirectional motion, in one or N coordinates alike, you would expect just what you see for the fluctuations. In fact, it's not really fluctuation then. 10 ns is also pretty short for a simulation of a protein. It's likely that you