[gmx-users] PBC correction to visualize a protein-membrane structure

[Justin Lemkul]

On 5/16/14, 4:04 AM, Juan Munoz-Garcia wrote:
> Dear GROMACS users,
>
> I’m preparing a protein-membrane structure to use as input for MD. I’ve just
> carried out a short minimisation of the lipids applying restraints to the
> protein, after which I’ve obtained the attached structure. I’ve tried all
> types of trjconv combinations with -pbc -ur or -fit, but it doesn’t work, I
> still get the same structure. Even more weird is that when I turn on the
> periodic images option in vmd I still don’t see the right protein embedded
> into the lipid bilayer. As this can’t be a real effect of minimisation, I'd
> like to ask for your advice.
>

The mailing list does not accept attachments.  Please post links to images or 
files to download.  An exact sequence of commands would be useful, as well.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================