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
V-rescale as thermostat does give approximately the correct value for Cp.
Thanks!!
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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,
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