[gmx-users] Npt equilibration of the membrane-mimicking CCl4 layer

Justin A. Lemkul jalemkul at vt.edu
Mon Feb 6 12:51:48 CET 2012

James Starlight wrote:
> Justin,
> I've built my system in accordance to the first way from your Biphgastic 
> system tutorial.
> I've defined system with slight biger (  on 1 nm in each dimension) 
> dimensions that I needed and place maximym CCl4 molecules in that box by
> genbox -ci ccl4.gro -nmol 900 -box  9.6 7.5 4 -o new_box.gro
> So I've supposed that I've defined maximum density for such box. How 
> else I could specify starting density of my box?

Some simple calculations using the desired density and the box dimensions (to 
get the volume) will tell you exactly how many molecules you need.  If you only 
"suppose" you've got a reasonable number, there are better ways to be sure ;)

> 2) I've tried use 1.4 VDV cutoff and crash of my system happened almost 
> alfter first 0.5 ns of simulation. By the way in the KALP tutorial I've 
> found Cutoff = 1.2. Why in that case you've used such uncommon values ?

We have demonstrated that this value is acceptable for such systems.  The lipid 
force field model was derived using 1.0 nm cutoffs, and Gromos96 with a 0.8/1.4 
nm twin-range scheme.  When combining these particular force fields (which can 
be done in this case), we had to find a set of values that would reproduce the 
behavior of each parameter set.  The value of 1.2 nm sufficiently reproduced the 
behavior of both, when combined.  Without such justification, one should not 
alter cutoffs.



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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