[gmx-users] RE: value of d in editconf

[Justin A. Lemkul]

alkasrivastava at iitb.ac.in 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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-- 
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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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