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

[Abhinav Agrawal]

Hi,

After applying energy minimization most of the atoms leave the box ( around
95%).

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.

I am not using any solvent in the system. Could that create a problem?

Or could the problem be that the box dimensions are too small? In that case
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.

------------------------------
>
> Message: 3
> Date: Thu, 4 Apr 2013 14:05:31 +0800 (CST)
> From: "song.yongshun" <song.yongshun at 163.com>
> Subject: Re:[gmx-users] Applying periodic boundary conditions in
>         energy  minimization
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID:
>         <48b65938.13820.13dd3a668a3.Coremail.song.yongshun at 163.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi,
> Actually you have already applied pbc,and there seems nothing wrong.
> Some atoms are out of the box is common.
> If your box vector is correct,then Gromacs will run successfuly afterwards.
> At 2013-04-03 22:51:54,"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
> >
> >
> >
> >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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