[gmx-users] Randomly replace molecules with another molecule

[Justin Lemkul]

On 6/2/17 3:51 PM, Li, Shi wrote:
> Dear Gromacs users,
> 
> I am wondering if there is a better way to randomly replace some molecules
> in a system box with another type of molecule. For example, I have a system
> with 1000 molecule A as the solvent and I have another molecule B as the
> solute. I want to generate a series of systems with different concentration
> of B. Is there some gmx command to do that?
> 
> I tried to use gmx insert-molecuels, but then I will need to first create a
> series of system A in order to insert different number of B.
> I don't know if gmx genion could do that or not, as I tried to use this but
> I am not sure how to make the replacement with B as both of them are charge
> neutral.
> 
> If you have a better solution. Please let me know! Thank you!
> 

GROMACS does not have the ability to replace waters with molecules.  Determine 
the number of B that are needed in a given volume for a given concentration, 
insert with gmx insert-molecules, then solvate with A using gmx solvate.  No 
replacement necessary, and the math is trivial.

-Justin

-- 
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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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