On 9/18/12 9:21 AM, Bharath K. Srikanth wrote:
Hi all
While attempting to simulate the self assembly of a course-grained DSPC
lipids, I ran into a problem using the genbox command.
I first used genbox to create a box of 32 DSPC lipids, of dimensions 20 x
20 x 20 nm^3. The command used was
genbox -ci dspc_single.gro -nmol 32 -box 20 20 20 -try 500 -o 32lipids.gro
This gave me 32 lipids in a random configuration, as expected. I also ran
en energy minimization on this configuration, with no problems (the file
32minimised.gro contained the coordinates after minimisation).
However, when I tried solvating the box with course-grained water
molecules using genbox, the added water molecules were formed in a small
box, at the corner of the lipid box region, and not interspersed with the
lipid molecules. The command I used was
genbox -cp 32minimised.gro -cs water.gro -o lipidsandwater.gro -maxsol 192
-vdwd 0.21
What could the problem be?
You have a 20-nm cubic box (huge) and you're telling genbox to add only a
maximum of 192 water molecules. Given the constraints imposed, you should only
expect to see a small fraction of your box solvated. Remove -maxsol and try again.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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