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

[Ebert Maximilian]

Thanks for the reply. I think I can simulate it now. The only thing I don’t understand and this is in reference to my other post: OPLS/AA parameters for 2-propanol
How can the self-diffusion coefficient be a good measure for testing my parameters if for TIP3P water the self-diffusion coefficient ist 6 x 10^-9 m2 s-1 but the experimental value is around 2.3 x 10^-9 m2 s-1. So if even for a highly used water model the coefficient doesn’t fit how can I make any assumption about the quality of my parameters for 2-propanol?

Thanks



On Sep 10, 2015, at 5:15 PM, Phwey Gil <psg30 at case.edu<mailto:psg30 at case.edu>> wrote:

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<mailto: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<mailto: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<mailto: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<mailto:psg30 at case.edu>
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