[gmx-users] Applying periodic boundary conditions in energy minimization

[Tsjerk Wassenaar]

There is no outside of the box.

Tsjerk


On Wed, Apr 3, 2013 at 4:51 PM, Abhinav Agrawal <abhv.agrw at gmail.com> wrote:

> Hi,
>
> I have a polymer box on which I wish to apply energy minimization. However,
> when I do energy minimization runs to polymer chain unravels and goes out
> of the box. I guess this is because periodic conditions are not applied.
>
> My em.mdp file is:
>
> >
> > ;
> > cpp                 =  /usr/bin/cpp
> > define              =  -DFLEX_SPC
> > constraints         =  none
> > integrator          =  steep
> > nsteps              =  1000
> > ;       Energy minimizing stuff
> > ;
> > emtol               =  2000
> > emstep              =  0.01
> > nstcomm             =  1
> > ns_type             =  grid
> > rlist               =  1
> > rcoulomb            =  1
> > rvdw                =  1
> > Tcoupl              =  no
> > Pcoupl              =  no
> > gen_vel             =  no
> > pbc                      = xyz
>
>
>
> I used the following commands:
>
> grompp -v -f em.mdp -c mmt_pla.gro -o em -p system.top -maxwarn 2
> >
>
>
> >  mdrun -v -s em.tpr -o em.trr -c after_em.gro -g emlog.log
>
>
>
> Can you please tell me what I am doing wrong. Thanks in advance
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.