[gmx-users] MDrun rerun issue

[dodia]

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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