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

[Ebert Maximilian]

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> 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
> 
> -- 
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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