[gmx-users] how to make water moleculers disperse uniformly in box and why DMSO moleculers cannot position restrained

Justin A. Lemkul jalemkul at vt.edu
Sun Jun 1 12:58:23 CEST 2008

Quoting wang kelvin <wangkelvin64 at gmail.com>:

> Dear gmx user
> Could you help me to give some hints about the following ?
> First , i want to make a mixture of water and DMSO, so i put 512 DMSO
> moleculers and 14000 water moleculers in a box using genbox command . I
> expect water moleculers disperse uniformly in box from beginning , but water
> always stay one side of box. . Is there good way to make water stay
> uniformly in box?

What is the spacing between your DMSO molecules, and how did you generate your
configuration (showing exact command lines is always best)?  Is it such that
water cannot enter the space between the DMSO molecules?

> Second , to achieve this goal , i do position_restrained mdrun for DMSO
> several times ,and let water moleculers move to spce beween DMSO moleculers
> . Each time , DMSO moleculers cannot be position restrained , and run freely
> in box . So i add force constant in porse.itp file to great extent . however
> , DMSO moleculers move from one position to another as usual. I am sure i
> has define "-DPOSRES" in pr.mdp . So my second question is why DMSO
> moleculers move freely even under great force constant defined in porse.itp
> file?

If they're moving freely, you've done something wrong.  It would be better to
show us your posre.itp and relevant sections of your topology so we can
comment.  If we assume you've done everything right, you wouldn't be having
this problem!


> I will be very thankful to your any hints?


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list