[gmx-users] Creating a box of water with density 1000 g/l
jalemkul at vt.edu
Thu Sep 10 23:10:04 CEST 2015
On 9/10/15 5:01 PM, Ebert Maximilian 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.
Then you need the approach I suggested - add the number of molecules you want,
adjust the box size, and simulate with NVT.
>> 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 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
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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
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