[gmx-users] dmso-box

David spoel at xray.bmc.uu.se
Thu Sep 19 08:32:33 CEST 2002

On Wed, 2002-09-18 at 17:41, Karin Bettinger wrote:
> Hi all!
> I want to use the dmso-box included in the top-files from gromacs.
> Does anybody know why this box has only a density of about 790g/l, while
> experimental
> data are about 1100g/l ?  (If not I would simply decrease the size of
> the box till the density is 1100)
Please find the correct DMSO force field parameters and perform a 1 ns
simulation with pressure coupling. That should give you a good start.

> Do I have to change the dielectrical constant to the experimental value
> of dmso for the simulations?
No! epsilon_r should always be 1...

> Why doesn't genbox treat these files as solvent (command: genbox -cs
> dmso.gro ....), but always includes
> only this one box with 208 dmso-molecules? That means the number of
> molecules depends not on the box volume (like the waterbox) and the
> created box is not randomly filled.
For me this works fine:
 genbox -cs dmso -o out -box 5 5 5

it yields a box with 912 dmso molecules
> Thank you for any help and information!
> karin
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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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