[gmx-users] exact number of water

[Justin Lemkul]

On 5/5/18 7:30 AM, Alex wrote:
> Dear all,
>
> I want to create a box containing %80 water (spce), %12 molecule A and %8
> molecule B. Using the gmx insert-molecules, I have already the portions of
> A and B in a box, and using the gmx solvate I tried to solvate the box, but
> the gmx solvate inserts much more than the required %80 water molecules in

This should tell you that your box is inappropriately large. Adding the 
desired number of water molecules will leave void space, which could 
cause instability in equilibration. You should reconsider your box size; 
it should be straightforward to calculate an appropriate volume based on 
some approximations of density or molecular volume.

> that box. I also tried to put water by gmx insert-molecules but it could
> not put even a single water in that box.
> So, I was wondering how to put exact number (let's say 6000 SOL or at least
> around) of water in such box?

gmx solvate -maxsol 6000

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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