[gmx-users] membed in mdrun VERSION 5.0.4

[Justin Lemkul]

On 1/8/16 3:38 AM, Nash, Anthony wrote:
> Many thanks Justin, that’s solved it.
> 
> The simulation is now running, reporting that 8 POPC molecules and 12 SOL
> molecules have been removed. However, I have a bit of a problem. I don’t
> seem to be able to get the -membed option working on a parallel
> installation of gromacs, only serial. I assume parallel isn’t supported?
> 

No idea, but the -membed incorporation into mdrun is currently a very big hack
to make it work, so you should expect limited support for features.

> Secondly, with my .tpr file very different from my running .trr (due to
> removed molecules), I don’t know of a way of pulling out a single frame
> from the trajectory to see how the simulation is progressing. (I would
> have just taken the first frame as a .gro, downloaded the latest .trr, and
> thrown them both into VMD). Any thoughts?
> 

Does the program report which residues were removed?  If so, you can just remove
those from the coordinate file you had before.  Otherwise, no, probably not.
Like I said, big hack to get it working in the present version.

-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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