Hi Mark,
My main aim was to do surface tension calculations, which would involve
scaling the .gro file coordinates and then recalculating the energetics
for the system. For that, I am trying to extract trajectory frames and
recalc energy difference between modified and unmodified gro files.
Right now, I was testing that whether results from .gro and .trr files
do match or not
On 2018-01-30 11:10, Mark Abraham wrote:
Hi,
Good initiative, but unfortunately mdrun -rerun is unfit for pretty
much
anything connected with the velocities. See
https://redmine.gromacs.org/issues/1868 for the gory details.
The potential energy should be fine (unless you are introducing a
periodicity artifact in how you are using trjconv), but why are you
involving trjconv at all? gmx mdrun -rerun prdv.trr works.
Mark
On Tue, Jan 30, 2018 at 10:37 AM dodia <do...@mpip-mainz.mpg.de> wrote:
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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