Re: [gmx-users] Normal mode analysis of pure water

simon sangma wrote: Hi Justin, Are you suggesting that after thorough energy minimization, seperate .mdp file is to be used for NMA? In that case how would that output file (energy minimised file) be taken as an input file for the grompp and mdrun command (for NMA)? What ext

[gmx-users] Normal mode analysis of pure water

Hi Berk, I want to determine the vibrational frequencies of water (close to the experimentally observed values for the three modes). And then extend the analogy for more complex systems. ___ gmx-users mailing listgmx-users@gromacs.org htt

[gmx-users] Normal mode analysis of pure water

Hi Justin, Are you suggesting that after thorough energy minimization, seperate .mdp file is to be used for NMA? In that case how would that output file (energy minimised file) be taken as an input file for the grompp and mdrun command (for NMA)? What extension would the file have

RE: [gmx-users] Normal mode analysis of pure water

2009 19:20:19 +0530 From: simoniitc...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] Normal mode analysis of pure water Hi Berk, You mentioned that standard NMA techniques will not work for the liquid water system. Could you suggest the alternatives then

[gmx-users] Normal mode analysis of pure water

Hi Berk, You mentioned that standard NMA techniques will not work for the liquid water system. Could you suggest the alternatives then? ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users P

RE: [gmx-users] Normal mode analysis of pure water

:43 +0530 From: simoniitc...@gmail.com To: gmx-users@gromacs.org Subject: [gmx-users] Normal mode analysis of pure water Hi, I encountered the following remarks during normal mode analysis of pure water. Can someone please suggest a solution. mdrun_d -v -s water.tpr -o traj.trr -c confout.gro

Re: [gmx-users] Normal mode analysis of pure water

simon sangma wrote: Hi Justin, I tried altering the .mdp file (integrator = steep instead of nm) for energy minimization. But in that case the mdrun did not generate the Hessian matrix (nm.mtx) inspite of using the command twice. Energy minimization is not the s

[gmx-users] Normal mode analysis of pure water

Hi Justin, I tried altering the .mdp file (integrator = steep instead of nm) for energy minimization. But in that case the mdrun did not generate the Hessian matrix (nm.mtx) inspite of using the command twice. ___ gmx-users mailin

Re: [gmx-users] Normal mode analysis of pure water

simon sangma wrote: Hi, I encountered the following remarks during normal mode analysis of pure water. Can someone please suggest a solution. You've been told twice already what the likely solution is: Maximum force: 2.74758e+03 Maximum force probably not small enough to ensure that

[gmx-users] Normal mode analysis of pure water

Hi, I encountered the following remarks during normal mode analysis of pure water. Can someone please suggest a solution. mdrun_d -v -s water.tpr -o traj.trr -c confout.gro -e ener.edr -g md.log -mtx nm.mtx Getting Loaded... Reading file water.tpr, VERSION 4.0.4 (double precision) Loaded with