[gmx-users] exact number of water
jalemkul at vt.edu
Sat May 5 14:25:37 CEST 2018
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 A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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