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

Saumyak Mukherjee mukherjee.saumyak50 at gmail.com
Mon May 29 08:17:31 CEST 2017

Hi Dilip,

To fix the amino acid at the centre of the box first you have to use -c
flag with editconf. Later, during simulation you have to use
define=-dposres in the mdp file. This will include the position restrain
defined in the posre.itp file generated during the use of pdb2gmx.


On 29 May 2017 at 10:59, Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:

> 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,
> Ph.D Student
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*Saumyak Mukherjee*

Junior Research Fellow
Prof. Biman Bagchi's Group
Solid State and Structural Chemistry Unit
Indian Institute of Science
Bangalore - 560012

Mob : 8017292426
Alternative e-mail : saumyakmukherjee at gmail.com
                                smukherjee at sscu.iisc.ernet.in

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