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 <[email protected]
<mailto:[email protected]>> 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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--
========================================
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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