[gmx-users] Simulating a protein dimer

[jkrieger at mrc-lmb.cam.ac.uk]

I solved the problem by using an em.tpr with pbc nojump for my dimers. pbc
whole takes the monomers as whole units and does as you described. pbc
nojump starting from md.tpr like I'd normally do didn't work because
partial boundary crossings had happened before the production md.

> I encountered similar problem after simulating a pentameric model of
> protein. It was solved by applying pbc whole in gmx trjconv.
>
> Sent from my iPhone
>
>> On 07-Jun-2016, at 7:49 pm, Biplab Ghosh <ghosh.biplab at gmail.com> wrote:
>>
>> Dear Gromacs Users,
>>
>> I am trying to simulate a protein dimer using Gromacs-5.1.2. Gromacs
>> completed successfully
>> but when analysing the trajectories, the monomers are flying apart and
>> coming back again!
>>
>> I used the following Gromacs commands/options:
>>
>> gmx trjconv -s protein-md.tpr -f protein-md.xtc  -pbc mol -center -ur
>> compact -o protein-md-center.xtc
>>
>> gmx trjconv -s protein-md.tpr -f  protein-md-center.xtc -fit rot+trans
>> -o
>> protein-md-center-fit.xtc
>>
>> gmx trjconv -s protein-processed.gro -f protein-md-center-fit.xtc -o
>> protein-movie.pdb -tu ns -dt 1
>>
>>
>> I would really appreciate any help on this.
>>
>> Regards,
>> Biplab.
>>
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