[gmx-users] minimum size for systems

[K.A. Feenstra]

Christoph Freudenberger wrote:
> 
> Hi there,
> 
> I am running simulations of organic salts (org. kation/Cl- anion)
> in variuos solvents. I am studying systems of different size
> In spc water everything went fine. The smallest box I was able to
> simulate (using an NPT ensemble) contain 1 ionpair and 91 spc's in a
> cubic box of about 1.45nm.
> A system of 1 ionpair, 50 spc's in box of 1.15nm crashed ('Command
> terminated abnormally.'), possibly because the cutoff's are getting to
> small in a system like that.
> Although a simulation of pure spc in the same box was possible.
> 
> Now I switched over to DMSO as solvent. Here the smallest box i
> can simulate contains 1 ionpair and 440 DMSO in a box of 3.7nm!
> All smaller systems I tried, crashed with the same error massage (see
> above). Decreasing the timestep from 2fs to 1fs made the simulations
> a more stable, but see some ugly 'spikes' in the total energy
> and temperature.
> 
> I attached the mpd and xvg of total energy and temperature of a system
> containing 1 ionpair and 28 DMSO (box: 1.45nm).
> The total energy and temperature for the larger DMSO system mentioned
> above are smooth.
> 
> Any hints what's going wrong?

A few guesses: it seems to be linked to charges in the system, DMSO
is more polar than SPC. This makes sense, since charge-related energy
drift will increase (drastically) with decreasing cut-off. So, I'd
guess you're just out of luck on this: you need a minimum cut-off to
get sensible energies, and that determines your smallest possible box.

Having said that, have you tried increasing the PME order? This might
make the transition from short-range (explicit) forces to long-range
(PME) charges smoother.


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
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| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
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| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
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