[gmx-users] dmso-box

Christoph Freudenberger christoph.freudenberger at chemie.uni-ulm.de
Thu Sep 19 09:28:35 CEST 2002

David wrote:
> 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
>>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.
The box you get from this will be signifficantly smaller than what
you started from.
If you need a box of defined size (i.e. 5nm box length) calculate the
number of molecules you need to fill this box to achieve the correct
density. Then generate a first box the normal way.

	genbox -cs dmso -o setup_1 -box 5 5 5

Check the number of molecules and add the missing ones (single_dmso.gro
has the geometry of just one single dmso-molecule):

	genbox -cp setup_1 -ci single_dmso -nmol x -try 50 -o setup_2

Now you can erform you equilibration with pressure coupling. The box 
usally shrinks a little bit, but no more than 0.05 nm.

Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm

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