[gmx-users] Creating a box of water with density 1000 g/l

[Phwey Gil]

I think I would do it this way.

Use L that is slightly larger than 2.494 so that you can fit all of the
512 water molecules you want. Then run a very short simulation at 10 bar.
The size of the box now should be less than 2.494.

Now change the box size to 2.494 and then run the final equilibration step
with NVT ensemble.

Run the simulation and then see if you get 1 bar!

On Thursday, September 10, 2015, Ebert Maximilian <m.ebert at umontreal.ca>
wrote:

> The reason is that I try to reproduce the experiment from the paper
> System-Size Dependence of Diffusion Coefficients and Viscosities from
> Molecular Dynamics
> Simulations with Periodic Boundary Conditions.
>
> before calculating the self diffusion coefficient for my organic solvent i
> wanted to see if my system setup is correct. the authors used 33 water
> molecules per nm^3. Therefore, I try to create a box in GROMACS with
> L=2.494 and fit 512 molecules of TIP3P water in. The reason the authors
> used these 33 molecules is to get about 1bar during the NVT without
> barostat.
>
> Max
>
> > On Sep 10, 2015, at 4:56 PM, Justin Lemkul <jalemkul at vt.edu
> <javascript:;>> wrote:
> >
> >
> >
> > On 9/10/15 4:44 PM, Ebert Maximilian wrote:
> >> Hi there,
> >>
> >> I am wondering if there is a better way to create a box with water of a
> certain size than:
> >>
> >> gmx solvate -cs spc216.gro -o water_box.gro -box 2.5 2.5 2.5 -maxsol 512
> >>
> >> To get a density of roughly 1000 g/l i would need to add 512 molecules
> in such a box. But the script only adds 502. I could play with the scale
> parameter but sometimes I have problems during minimization with messages
> like:
> >>
> >> Water molecule starting at atom 1465 can not be settled.
> >> Check for bad contacts and/or reduce the timestep if appropriate.
> >>
> >
> > The density will anyway be dictated by the water model itself; none of
> the common ones achieve exactly 1000 g/L.  In principle, you could expand
> the box very slightly, then re-size the box and simulate with NVT (thus
> constant density), but at that point you're really manipulating the
> outcome, and I don't know why you would need to go to such lengths.
> >
> > -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 <javascript:;> | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
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-- 
Dan Gil
Case Western Reserve University | Class of 2016
Researcher, Department of Chemical Engineering
psg30 at case.edu