[gmx-users] editconf -d

[Justin A. Lemkul]

mohammad agha wrote:
> Dear Prof.
> 
> May I know the best quantity for -d option in editconf program? for 
> example for a cubic box consists of 70000 water molecules and 500 
> surfactant molecules with 22 , 022 , 22 box dimensions in x , y and z?
> 

If you've got a box built, what's the need for -d?  The purpose of setting a 
value with -d is to define a unit cell around a solute such that it does not 
interact with its periodic image during the simulation.  The value is, to some 
extent, controlled by the cutoff values used during MD.

-Justin

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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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