[gmx-users] Comparing two Ptn-Ptn docking models

[Justin Lemkul]

On 3/10/15 11:59 PM, Diogo Martins de Sá wrote:
> Thanks for the advice Justin!
>
> I'm looking in to it right now.
>
> My box has the following dimensions:
> 9.10300  12.10200  11.46200
>
> How would you define "continuous pull", is it pull in which the distance
> increases indefinitely but slow enough not to trespass the distance
> limits/conditions? I get the part where the periodic images can't

There's no real "limit," per se, but you need to decide on a suitably long 
reaction coordinate to achieve separation of the proteins.

> interact and the "less than one half the length of the box" condition.
> But how do I know if my box and my system are apt for umbrella sampling?

Decide on the length of the reaction coordinate that will be sufficient to 
separate your proteins, translate one subunit out that far (editconf or trjconv) 
and build a box around it of suitable size.  That's the size you need for every 
window (the system doesn't change between windows).

> will I be able to use mdrun -rerun with my current system?
>

No, umbrella sampling is a totally new set of simulations.

-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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