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

[Justin Lemkul]

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

========================================