[gmx-users] 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



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