[gmx-users] membed in mdrun VERSION 5.0.4

[Mark Abraham]

Hi,

The current implementation of membed is quite sane and should support all
kinds of parallelization. (It is difficult to say much that is nice about
the first implementation, though!)

gmx trjconv and convert-tpr are good for making subsets from well chosen
index groups.

Mark

On Fri, 8 Jan 2016 13:35 Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> --
> ==================================================
>
> 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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