[gmx-users] Problems

Justin A. Lemkul jalemkul at vt.edu
Sat Dec 5 16:50:34 CET 2009

pawan raghav wrote:
> When defining the box dimention then how do I know about the distance of 
> protein from the box wall? Which should be greater than half of the 

You know because you specify it with editconf -d :)

> Cut-Off (1.4nm) (according to some tutorial).

This solute-wall distance is not the one that is related to the cutoff 
(directly).  It is the size of the resulting box that is of concern.

> Then what are longest cutoff which must be shorter than half the 
> shortest box vector to satisfy the minimum image convention. I am 
> asking because I have run gromacs from default parameter of some other 
> tutorial. I have used 0.75 value for -d when using editconf.

The cutoffs are what you specify in the .mdp file (rcoulomb, rvdw) - these must 
be less than 1/2 the shortest box vector.  As for how you design the box, that 
will be dependent upon the size of the solute.  For most globular proteins, the 
choice when running editconf -d is not terribly sensitive, although one usually 
sees a value of ~1.0 nm used in the literature.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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