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

[song.yongshun]

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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