[gmx-users] minimum size for systems

Christoph Freudenberger christoph.freudenberger at chemie.uni-ulm.de
Fri Sep 27 11:44:57 CEST 2002

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?

Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785
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