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

[Justin Lemkul]

On Wed, Apr 3, 2013 at 10:51 AM, 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
>
>
This last line means PBC are being applied. Your observations are
consistent with using a box that is too small for the solute, but since you
haven't supplied information as to (1) what the system is, (2) how you
built it, or (3) how large the box is, there's very little to say beyond
speculation.

-Justin

-- 

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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540)
231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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