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

wang kelvin wangkelvin64 at gmail.com
Sun Jun 1 12:31:45 CEST 2008

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?

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

I will be very thankful to your any hints?
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