[gmx-users] NVT and NVE

JMandumpal jesbman at rediffmail.com
Fri Mar 28 02:51:31 CET 2008

Dear gromacs users,

I ran 100ps equilibraion, NVT, prior to running 60ps NVE to check the energy conservation with different timesteps: 1.0fs, 1.5fs and 2.0fs, but  these NVE simulations seem not to converge even after. Following is the command I used for running 60ps NVE :
grompp_d -np $PBS_NCPUS -f mdout_NVE.mdp -p topol.top -c conf_100.gro -o binary.tpr
mpirun mdrun_mpi_d -s binary.tpr -o pr.trr -c output_1.gro -g topol.log
conf_100.gro is the equilibrated box, from my 100ps NVT, which I used for the NVE's. Is this the right way of doing it? or Am I miss something else in those commands.
My system is 500 TIP5P box.


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