JMandumpal wrote:
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.
Well the pertinent parameters are all in the .mdp file, so we can't
tell. Certainly you are not doing an exact restart
(http://wiki.gromacs.org/index.php/Doing_Restarts), and so must be
re-generating velocities, which removes some of the value of the NVT
equilibration. Changing ensemble requires a re-equilibration period, but
you should attempt to minimize the severity of the transition by doing
the restart from the .trr file with velocities, and not a .gro file that
(presumably) lacks velocities and has low-resolution coordinates.
Your second query about using tpbconv will not work - the tpbconv
restarts preserve the ensemble.
Mark
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