[gmx-users] Simulating a protein dimer

[sun]

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.
> 
> --
> "Simplicity in life allows you to focus on what's important"
> -- 
> 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.