[gmx-users] MDrun rerun issue

dodia dodia at mpip-mainz.mpg.de
Tue Jan 30 12:02:20 CET 2018

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 <dodia at 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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