[gmx-users] bonded forces in output

[Justin Lemkul]

On 9/26/15 5:31 AM, Stanislav Šimko wrote:
> Dear gromacs users,
> I'm writing my code to calculate pressure from trajectory files - from
> problthat em atomic positions and forces - according to virial theorem.
> Currently, I'm able to calculate the same pressure when I've got only
> non-bonded forces of a small system (10 atoms with charges and LJ
> parameters) centered in a big (100nm cubic) box. Hopefully, my code
> should work also for smaller box where atoms can see periodic images.
> The problem that I'm facing right now is that I do not know how to
> obtain bonded forces from the trajectory files. E.g., for single spc
> water molecule gromacs gives zero forces on all atoms, even though I
> assigned them different velocities.
> 	to obtain forces I run:
> 	gmx traj -f *.trr -s *.tpr -of forces -fp
>   Also, gromacs gives me non-zero virial (diagonal elements XX, YY, ZZ),
> which means that there are some forces
> 	gmx energy -f *.edr -s *.tpr ...
> So I would like to ask, if there is some way how to get bonded forces
> out of the trajectory... (or rerun with some runtime parameters to
> force gromacs to print bonded forces)

By default, water is treated as rigid via SETTLE, so there are no bonded forces. 
  You can turn this off with "define = -DFLEXIBLE" in the .mdp file for the 
purpose of do a re-calculation of energies and forces.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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