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

[Tsjerk Wassenaar]

Hey :)

I'll make a try to be a bit more constructive :p
First of all, always try to think out of the box, especially with PBC :D
The problem may be due to overlapping atoms/molecules, pushing each other
out during energy minimization. When merging boxes, be careful not to
introduce overlaps, by 1. asserting that all molecules are whole at the
start (because the new PBC cannot correct the breaks due to the old PBC),
and 2. molecules "sticking out" on one side (any side) of the box are not
placed onto molecules from the box it is merged with, and vice versa. Also,
always inspect the results visually.

Hope it helps,

Tsjerk



On Thu, Apr 4, 2013 at 10:14 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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<http://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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
>
> --
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-- 
Tsjerk A. Wassenaar, Ph.D.