[gmx-users] Diffusion coefficient of metal complex

[Justin Lemkul]

On 7/23/14, 7:13 AM, Meena Singh wrote:
> Dear GROMACS users,
>
> I'm working on the diffusivity of metal ion with its ligand in organic
> phase.
>
> I want to calculate the diffusion coefficient of metal-ligand complex as a
> group, but when I run g_msd command the option are there for only
> individual molecules diffusivity calculation.
>
> Can I calculate the diffusion coefficient of specific complex from the box
> which contains metal ions and ligand molecules.
>
> Does anyone have a suggestion to help me with this problem?
>

Create an index group for whatever subset of atoms you like and use it for the 
calculation.

-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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