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

[Peter Kroon]

Hi,


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.


Peter


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,
>>
>> DILIP.H.N
>> Ph.D Student
>>
>>
>>
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>> referral=cy16f01.dilip at nitk.edu.in&idSignature=22>
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>
>