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

[Debraj Das]

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

With regards
Arya Das


On Mon, Jun 5, 2017 at 7:58 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
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> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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