[EMAIL PROTECTED] wrote:
Hi
I am doing a 5 peptide(7 residue) simulation in a 5 nm cubic box. but
during editconf i haven't given the option -d to specify the distance
between the solute and the box. Now some of the atoms of my peptides are
out of the box also is it normal? Does not applying -d is going to effect
in any way.
If the peptides are moving "out of the box" during the simulation, this is
normal behavior of PBC. If they are sticking out of the box before running any
MD, then you may have a problem.
Specifying -d ensures that you adhere to the minimum image convention. If, in
preparing your system, you somehow manually generated a box that suffices to
keep periodic images from interacting with each other without using editconf -d,
then everything is fine. But do check to make sure you don't have PBC artefacts.
-Justin
Thanks
Alka
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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