[gmx-users] force calculation

[Justin Lemkul]

On 5/9/16 7:24 AM, mahdiyeh poorsargol wrote:
> Dear gromacs user,
> Does anyone know how to calculate the force exerted on the particle in the
> simulated system from the output files?
> I simulated  a system including two parallel surfactant-covered graphene
> sheets, separated with the inter-sheet distance of 34.0 Å. I want to
> compute the force average which need to hold them at the current location
> or force exerted on a graphene sheet.
> Can anyone suggest a method?

Forces are saved in the .trr and extracted with gmx traj.  If you didn't save 
forces (nstfout > 0) then use mdrun -rerun on whatever existing trajectory you 
have with a new .tpr specifying the desired output.

-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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