[gmx-users] Regarding centering the molecule/protein during Simulation

[Dilip H N]

Hello,
I have ran a md simulation of a amino-acid with solvent mixture. Now i view
the trajectory in vmd and see tht the amino-acid moves sometimes toward the
edge of the box,sometimes towards the corners and so on...
 Now how can i centre only the amino-acid to the centre of the box and rest
(ie.,solvent mixture) to move as it is..ie., if i view the trajectory in
vmd i want to fix only the amino-acid to be in centre,whereas the solvent
mixtures to move around during the trajectory...
How can i do this,...??

Thank you...

-- 
With Best Regards,

DILIP.H.N
Ph.D Student



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