[gmx-users] where are the forces?

[Albert Solernou]

That was fast!!

Thanks Justin, the forces are effectively there and I am getting them out.

Cheers,
Albert


On 04/02/2015 05:21 PM, Justin Lemkul wrote:
>
> On 4/2/15 12:18 PM, Albert Solernou wrote:
>> Hi,
>> I am trying to get a trajectory that include forces... but I am not sure I am
>> getting it. My .mdp file has the following lines:
>>    nstxout         = 500           ; save coordinates every 1.0 ps
>>    nstvout         = 500           ; save velocities every 1.0 ps
>>    nstenergy       = 500           ; save energies every 1.0 ps
>>    nstfout         = 500           ; save forces every 1.0 ps
>>    nstlog          = 500           ; update log file every 1.0 ps
>> but because the trajectory is saved in a .trr file... it is difficult to know
>> whether the forces are there or not.
>>
>> Therefore, I turn my .trr trajectory into .gro, to see what is in there:
>>    gmx trjconv -vel -force -s gmx.tpr -f gmx.trr -o gmx.gro
>> and I expect to see 9 numbers after every atom, but there are only 6... and when
>> I "trjconv" using "-novel", then only 3 numbers are there.
>>
>> So the question is: where are the forces? Were they saved at all?
>>
> gmx check -f gmx.trr will tell you.
>
> The forces won't be written to a .gro file; those are coordinate files that hold
> only coordinates or velocities.  You can extract forces using gmx traj.
>
> -Justin
>

-- 
---------------------------------
   Dr Albert Solernou
   EPSRC Research Fellow,
   Department of Physics and Astronomy,
   University of Leeds