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
--
========================================
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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