Re: [gmx-users] Can I customize Gromacs (e.g., on-fly-analysis) with multi-threading enabled?

, Peng On Mon, Oct 4, 2010 at 7:55 PM, Mark Abraham mark.abra...@anu.edu.au wrote: - Original Message - From: 吴鹏 geroge...@gmail.com Date: Tuesday, October 5, 2010 3:24 Subject: [gmx-users] Can I customize Gromacs (e.g., on-fly-analysis) with multi-threading enabled? To: Discussion

[gmx-users] Can I customize Gromacs (e.g., on-fly-analysis) with multi-threading enabled?

Dear All: I am trying to do trajectory analysis on-the-fly and encountered some difficulty. What did I do: I inserted a small piece of code into md.c to READ the position of atoms and do some simple analysis. In the GMX3.2, my code works fine. The problem: In GMX4.5.1, my code works only if I

[gmx-users] Fail to reproduce shifted VDW

Hello GMX users, I want to reproduce the shifted VDW force done by Gromacs but the efforts is in vain. The result given by Gromacs was slightly different(1*10^-3 depends on the atoms distance) form the result got from the way suggested by the manual. I tested a case in which there are two atoms

Re: [gmx-users] eliminating forces on certain direction

Hi Mark, Haha. Yes, your words is right. My objective is to study the interaction between ions and walls. I think the ions may be attached in the wall so the velocity getten from MD simulation is always bigger than the continuum theory's prediction. So I want to build a simulation on which ion

Re: [gmx-users] eliminating forces on certain direction

Hi Mark, What you said reminds me to think deeply about my speculation. Thanks for your remind and I hope to discuss it with you when I get some ideas on that. Peng Wu On Tue, Oct 13, 2009 at 10:02 AM, Mark Abraham mark.abra...@anu.edu.auwrote: 吴鹏 wrote: Hi Mark, Haha. Yes, your words

[gmx-users] eliminating forces on certain direction

Hi GMX users, I am doing a modified simulation which requires to eliminate an interaction at certain direction while remain the interaction at other directions. Since the itp files contain the C6 C12 of the interaction, it is impossible to only remain the interaction a one direction while

Re: [gmx-users] bypassing pdb2gmx

Use editconf to change gro file type to pdb file. On Wed, Sep 9, 2009 at 8:29 PM, Amit Choubey kgp.a...@gmail.com wrote: hi everyone, I have a pdb file of my system and i want it to be fed into the GROMACS software. I have a new force field for the simulation and i have made the .top file