Dear gromacs users,
I am new user and trying to learn about the software by running simple
water box simulations. I did a 15ns NVT simulation of around 80 water
molecules (after 1.5ns+1.5ns of NVT & NPT equilibration) at 300K and the
resultant data seemed reasonably accurate wrt density and average
temperature. Now I tried to extract 50 frames from the trajectory and
stored them in a .gro file (with positions+velocities) and tried to use
mdrun -rerun to crosscheck energies, but in the resultant log file, the
temperature varies around 7000K, potential energy becomes positive and
other values go haywire. Can anyone help me with this issue? I used the
following commands after production calculation:
echo 1 | gmx trjconv -f prdv.trr -s prdv.tpr -vel -dt 100 -box 1.32 1.32
3.5 -o frame.gro
gmx mdrun -s prdv.tpr -rerun frame.gro -g test.log
prdv is the file suffix for production simulation. prdv.trr contains all
the positions, velocities and forces at every 1.5ps
Best Regards,
Mayank Dodia
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