From: Neelanjana Sengupta (senguptan_at_gmail.com)
Date: Tue Oct 24 2006 - 09:58:09 CDT
Hi,
I was thinking your simulation was for just a box of water. If you have a
protein in it, then 'wrapAll on' may not be a good idea. You should do pbc,
and during analysis, make sure you calcualte distances with the
min.imagesconvention. You don't really care how you box of solvent
'looks', per se.
However, to understand why your box is getting deformed inspite of wrapAll,
you'll have to do short experimental simulations with a bunch of stuff to
see what's the issue. What did you mean by 'constraining protein to move'?
Hi all,
> I am constraining my protein to move during the equilibration. is
> this the reason for deformed water box?
>
> > Hi all
> > I am heating my system (protein solvated in water box) after
> > energy minimization to 300 K. but after heating, i am getting a deformed
> > water box. In my configuration file, i am using Periodic Boundary condition
> > and wrapall on still i am getting deformed box. is this deformation of water
> > box is related to heating or is there any problem in my configuration file?
> >
> >
> >
> > --
****************************************
Neelanjana Sengupta, PhD student
Dept. of Chemistry
Univ. of California-Irvine
Irvine, CA 92697
USA
Phone: 1-949-824 9921
email: sengupta_at_uci.edu
****************************************
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