[gmx-users] box of methanol

David van der Spoel spoel at xray.bmc.uu.se
Thu Jul 25 20:50:04 CEST 2002

On Thu, 25 Jul 2002, Luca Monticelli wrote:

>I used the G43a1 force field, with
>cut-offs 0.8/1.4 (Gromos-96 was
>parameterized with these twin-range
>cut-offs, right?) and NPT conditions;
>box size is approximately 4.3*4.3*4.3,
>timestep=2fs, nstlist=5, no constraints,
>compressibility= 4.575e-4; total time is
>5 ns.
>These are the results.
>It takes ~500 ps for the pressure to 
>become relatively stable.
>Excluding the initial 500 ps, the 
>average d=749, with
>an RMSD of 3.9.
>If I change the cut-offs to 0.9/1.4, 
>leaving all other
>parameters identical, I find d=782, with
>an RMSD of 3.5. Not bad, the error is 
>only ~1.1%.

This is a serious difference. I guess you are not running with dispersion
correction, use
dispcorr = enerpres, that will make the difference between the two
simulations smaller, and also contract your box slightly more.
Furthermore a timestep of 2 fs is too long if you are not using
constraints. If you really object to using all constraints, you should go
down to 0.5 fs, or 1 fs when you constrain only the H.

>If anybody is interested in using this 
>box, just let me know.
It would also be interesting to compare the results to the all-atom OPLS
model that was posted on the list recently.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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