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

[Abhinav Agrawal]

> > 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
>
> --
>
> ========================================
>
> 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
>
> ========================================
>

I am using a composite system of polymer and clay. The composite box (5.8
nm * 5.8 nm *7 nm) is made from combining a polymer box (5.7 nm * 5.7 nm *
5.7 nm) and clay box (5.5 nm * 5.1 nm * 1 nm) using editconf and genbox.

Should I increase the size of the composite box. Also, If I increase the
size of the box how do I ensure that the density of the system does not
chance. Thanks for your help.