[gmx-users] topology file

I create a parallel job file with the following content #$ -N prep66 #$ -pe openmpi* 12 #$ -cwd #$ -q medium* mpirun -np 12 /data/apps/gromacs/4.6.1/mpi/bin/editconf_mpi -f 66.pdb -o cnt.gro -bt cubic -box 5 5 5 -c mpirun -np 12 /data/apps/gromacs/4.6.1/mpi/bin/g_x2top_mpi -f cnt.gro -o cnt.top

Re: [gmx-users] Rigid water model

V-rescale as thermostat does give approximately the correct value for Cp. Thanks!! -- View this message in context: http://gromacs.5086.x6.nabble.com/Rigid-water-model-tp5015158p5015202.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list *

[gmx-users] Rigid water model

Hi! I tried to reproduce results for rigid water with 895 molecules~1000 kg/m3 density, 10 ns NPT simulation (298 K 1 bar)with Parinello Rahman Barostat and Berendsen thermostat. Here is my result for SPC water Kappa (J/m3)5.689E-10 Cp 22.8054 Cp- Cv 5.94102 The density,

[gmx-users] CNT in water

Hi, I am trying to simulate a simple system of CNT in bulk water. The steps that I have completed are: 1. Create a pdb file for CNT. 2. Use editconf to convert to a gro file and define the length of the simulation box, the pbc etc. 3. Create a forcefield folder in my current working