James Starlight wrote:
Justin,
2012/2/6 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@vt.edu>>
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 ;)
In accordance to my calculations I need in ~ 1000 CCl4 to obtain 1.600
g/cm^-3 density with my box dimensins
By the way way I try to define such system by
genbox -ci ccl4.gro -nmol 1000 -box 8.6 6.5 3 -o ccl4_box.gro
I've obtain memory error :(
Is there any other way to define such system with the desired size and
n_mollecules with the less computation demands?
Two options:
1. Add them incrementally to the box (100 at a time or so, until the desired
value is reached)
2. Build a small box of solvent (a few hundred molecules), then use genbox -cs
instead of -ci to use the small solvent box to create the one of desired size.
-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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