[gmx-users] Generation of density curve for biphasic system

[Justin Lemkul]

On 6/6/17 2:16 AM, Debraj Das wrote:
> Dear Justin,
> I am getting error with
> gmx_mpi densorder -s topol.tpr -f traj.trr -n index.ndx -o density.dat
> 
> It will not write anything in that file.

If you want help solving this, you have to tell us exactly what the error was.

> I have also tried gmx density , but it is giving the overall density
> profile not for the individual phase.

You can get the density of any subset of the system by providing an appropriate 
index group.  gmx density prompts you to select what you want computed, so if 
you select System you won't get what you want.  But if you select each of the 
phases separately, you will.

-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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