[gmx-users] Simulating a protein dimer

[Tsjerk Wassenaar]

Hey :)

There's a suggested workflow on the Gromacs site:

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Cheers,

Tsjerk
On Jun 7, 2016 11:50 PM, <jkrieger at mrc-lmb.cam.ac.uk> wrote:

> 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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