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

[Abhinav Agrawal]

I have a clay pdb file
http://s24.postimg.org/je3mvov9h/MMT.png

and a polymer structure file:
http://s24.postimg.org/ei003zv45/PLA.png


I use the following commands to generate a composite box

> genbox -cp mmt.pdb -o mmt_box.gro

> editconf -f mmt_box.gro -o mmt_newbox.gro -box 5.800 5.811 7.5 -center
2.499  2.658  0.647

> genbox -cp pla.gro -o pla_box.gro

> editconf -f pla_box.gro -o pla_newbox.gro -box 5.800 5.811 7.5 -center
2.732  2.722  4.277

> genbox -cp mmt_newbox.gro -ci pla_newbox.gro -nmol 1 -o mmt_pla.gro -try
100

Image of composite box:
http://s24.postimg.org/w9g7w6zwl/MMT_PLA.png


After this I run the energy minimization using following commands

> grompp -v -f em.mdp -c mmt_pla.gro -o em -p system.top -maxwarn 1

> mdrun -v -s em.tpr -o em.trr -c after_em.gro -g emlog.log -nt 1


The structure after energy minimization:
http://s24.postimg.org/3l39syxqd/After_EM.png


Below are the links for em.mdp, and system.top

em.mdp : http://pastebin.com/3YsPR4FX
system.top : http://pastebin.com/2PXdPA9P


I hope this is everything you require. Thanks for you help.


------------------------------
>
> Message: 3
> Date: Thu, 04 Apr 2013 04:14:57 -0400
> From: Justin Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Re: Applying periodic boundary conditions in
>         energy  minimization
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <515D3681.30405 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> On 4/3/13 9:46 PM, Abhinav Agrawal 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
> >>
> >> --
> >>
> >> ========================================
> >>
> >> 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.
> >
>
> No, the box size seems reasonable.  I only suggested that because the
> behavior
> you described (unfolding of the polymer) seemed to indicate spurious forces
> across PBC.  As Tsjerk rightly noted, there's no such thing as "outside"
> of an
> infinite system.
>
> Without the exact sequence of commands and links to before and after
> images of
> the behavior you're seeing, there's not really much anyone can do to help.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>