[gmx-users] pulling of a molecule through protein-membrane system

Justin Lemkul jalemkul at vt.edu
Tue Aug 1 20:43:55 CEST 2017

On 8/1/17 10:01 AM, Alex Mathew wrote:
> Dear all gromacs users,
> I would like to build a protein-membrane system to perform umbrella
> simulation; I need to calculate the molecule transportation by pulling it
> from top to bottom. In the tutorial, it says  "Some force fields include
> everything you need. For instance, it is unwise to try to literally follow
> this approach for a force field like CHARMM36, as it needs no modification.
> In that case, you are much better off building the system with CHARMM-GUI
> <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/www.charmm-gui.org>
> .
> I want to use Charmm36 force field, but I did not see any option to make a
> box for US (as mentioned in US tutorial). Any suggestion how should I
> proceed?

Specify large enough box dimensions in whatever direction you want (probably z) 
when building the box.  There's no specific "build a system for umbrella 
sampling" because the only consideration unique to this case is the box size.



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


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