[gmx-users] Applying periodic boundary conditions in energy minimization
tsjerkw at gmail.com
Wed Apr 3 17:14:54 CEST 2013
There is no outside of the box.
On Wed, Apr 3, 2013 at 4:51 PM, Abhinav Agrawal <abhv.agrw at gmail.com> wrote:
> 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.
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