[gmx-users] Nonsymetric molecule across pbc

[Steven Neumann]

Thank you Justin. Indeed, the problem lies in maintaining the geometry... I
need to simplify the system for free energy calculations.

Steven


On Wed, Feb 19, 2014 at 1:31 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 2/18/14, 4:04 PM, Steven Neumann wrote:
>
>> Or maybe just 2 of them in the box: so that the one in the cell and
>> another one
>> has its quarter in the unit cell edge and the free energy between them?
>> Then
>> this PMF take into account all of the others being copied around. Would
>> US mdp
>> option wont complain?
>>
>>
> Worth a try.  This is a very complicated case that I doubt the pull code
> in Gromacs will deal with very elegantly.  You can easily define two
> vectors along which to pull (one tube is pull_group0 and the other two are
> pull_group1 and pull_group2, with relevant vectors for the biasing
> restraint).  That's a fairly simple 2-D PMF that can be done.  The problem
> is in maintaining the equilateral geometry that you desire.  To do that,
> you have to introduce a third restraint, which also somehow has to be
> debiased during WHAM.  The problem is it does not come from the pull code,
> so I honestly don't know how to deal with it within Gromacs.  You'll
> probably have to look into Alan Grossfield's WHAM program or something else
> entirely, like PLUMED.
>
>
> -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
>
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