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

[Tsjerk Wassenaar]

Hey Abhinav,

Your polymer seems to be one long molecule, which is made whole over PBC.
The result has nothing to do with EM.

Cheers,

Tsjerk


On Thu, Apr 4, 2013 at 11:37 AM, Abhinav Agrawal <abhv.agrw at gmail.com>wrote:

> 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
> >
> > ========================================
> >
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.