[gmx-users] How to define coordinates of protein and simulation box in the pulling simulation automatically?

[Justin Lemkul]

On 7/5/16 3:30 AM, Hassan Aaryapour wrote:
> Dear Justin A. Lemkul,
>
>
>
> How do you calculated the coordinates for center (3.280, 2.181, 2.4775) and
> box dimensions 6.560 x 4.362 x 12 in Umbrella Sampling by the following
> program:
>
> gmx editconf -f complex.gro -o newbox.gro -center 3.280 2.181 2.4775 -box
> 6.560 4.362 12.
>

I defined an original box that was 1 nm larger than any protein atom in all 3 
dimensions, and then took x/2, y/2, and sufficient space along z to pull as far 
as I needed to.

> When I calculate the geometrical center by chimera or accelrys discover
> studio for my protein complex, it was emerged from box edges. How to
> resolve it by softwares (not manually)?
>

I don't know what magic capabilities each program has, though there's no reason 
to do any of it outside of GROMACS.  The solution is system-specific, so I don't 
know that you can really get away from having to do something manually.  The 
initial box definition is done with editconf -d (automatic) but then the actual 
box vectors needed depend on the size of the proteins and the length of the 
reaction coordinate (something that needs to be set by the user).

-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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