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

Peter Kroon p.c.kroon at rug.nl
Mon May 29 10:01:10 CEST 2017


I would not do this. I would run my simulation as normal (no position
restraints), and center my amino acid in post processing (gmx trjconv
-pbc mol -center ...). You may need to make an appropriate index file.
Alternatively you may want to use -fit instead of -center, but that's a
matter of taste.


On 29-05-17 08:16, Saumyak Mukherjee wrote:
> 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.
> Best,
> Saumyak
> 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
>>   <https://mailtrack.io/> Sent with Mailtrack
>> <https://mailtrack.io/install?source=signature&lang=en&
>> referral=cy16f01.dilip at nitk.edu.in&idSignature=22>
>> --
>> Gromacs Users mailing list
>> * Please search the archive at http://www.gromacs.org/
>> Support/Mailing_Lists/GMX-Users_List before posting!
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list