[gmx-users] question about energy minimization

[Justin A. Lemkul]

Amit Choubey wrote:
> Hi Omer,
> 
> My question was to how to avoid the "diffusion" of molecules out of the 
> box during energy minimization and MD  run? I think what you suggested 
> here will just change the present trajectory into a new by using the pbc 
> condition.
> 

There is no "outside" in a periodic system.  EM should not be causing huge 
changes to your system; if particles are flying around chaotically, your system 
is probably not stable.

> But i am wondering shouldnt this be done in MD calculation itself. It 
> seems me to me that physics will be significantly different if i dont 
> put the particles which go out of the box, back into the box. In that 
> way the box will keep on expanding as i increase my simulation time and 
> the calculated equilibirium properties wont be very meaningful and will 
> fluctuate more than they really should.
> 

If you have inserted molecules into the system by force (if I recall the 
original post), you should expect the system to expand.  Omer's suggestion was 
post-processing for proper visualization; periodicity is accounted for in the MD 
calculation.

The box will continue to expand until it reaches equilibrium, if possible. 
After you obtain a stable box, you may be able to collect meaningful data.

-Justin

> By the way i am talking about long chain lipid molecules here and i am 
> using an all bond constraint.
> 
> Amit
> 
> 
> 
> On Tue, Sep 29, 2009 at 5:17 AM, Omer Markovitch <omermar at gmail.com 
> <mailto:omermar at gmail.com>> wrote:
> 
>     Trj "trjconv -pbc nojump", or "trjconv -h" and read the short help
>     printed. Omer.
> 
>      
> 
> 
>         I actually didnt realize this until i did a long simulation
>         after which the trajectories of some of the atoms looked way out
>         of the box dimensions. The co-ordinates of many atoms didnt lie
>         in the box range. Although the output file contained the same
>         box dimensions as I started with. Could someone help me in
>         understanding what happened?
> 
> 
> 
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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