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

[Justin Lemkul]

On 6/5/17 10:25 AM, Debraj Das wrote:
> Dear GROMACS user,
> 
> I am trying to get the profile of density at interface for water/dodecane
> biphasic system.
> 
> First I have prepared my index file with the command below
> 
> *gmx_mpi make_ndx -f confout.gro*  and it will genetare index.ndx.
> 
> Then I have tried the command for interface density
> 
> 
> *gmx_mpi densorder -s topol.tpr -f traj.trr -n index.ndx -o density.dat*
> But it will not write density.dat file.
> 

Why not?  Do you get an error?

> How the density profile can be generated ? Is there any other command to
> execute ? I need help in this regards.
> 

gmx density is probably the easier option here.

-Justin

-- 
==================================================

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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