Justin A. Lemkul wrote:
Fabian Casteblanco wrote:
Hello,
I was wondering if someone can help me with a general genbox question.
I have been using the command line:
genbox -ci octanol.gro -nmol 1000 -box 5 5 5 -o prop_1000.gro
to fill a box with 1000 molecules of octanol. With the smaller
n-alcohols, it worked fine but as I started using 1-butanol,
1-pentanol, (longer carbon chains) up to octanol, Gromacs sometimes
ends the command with a 'Killedin-Solvent overlap' line at the very
end. Sometimes increasing the box size helped, but for 1-pentanol,
even 7 7 7 box size didn't work. Also, do these killed runs take up
some sort of space. My memory space decreases a little bit even on
failed runs.
Generating random boxes in this way requires lots of memory and is prone
to failure. A useful strategy is to overestimate the size of the box so
that genbox doesn't have to do too many iterations to place all of the
molecules, then run a nice, long equilibration to get the box vectors
(and therefore density, etc) correct.
A more reliable method is probably genconf:
genconf -f molecule.gro -nbox 10 10 10 -o box.gro
You'll get 1000 molecules every time and the box size should be sensible. Then
proceed with equilibration.
-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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