Tandia, Adama wrote:
Dears,
I'm generating a box filled with NO3 molecules using Gromacs 3.3:
Any particular reason you're using software that is five years old? Unless
you've got a particular reason (i.e. continuity with older work), I'd strongly
recommend upgrading to version 4.0.7 for all the newest features and a major
speed upgrade.
genbox -ci molecule.gro -p molecule.top -o bigbox.gro -box 4.0 4.0 4.0
-nmol 800 -vdwd 0.2
The file bigbox.gro is generated but molecules are entangled. This makes
the geometry optimization to remove close contact impossible.
Any suggestions?
Have you tried a bigger box? Using a 5-nm box worked for me. When I tried the
same command you did, my machine ran out of memory, so it's probably a rather
complicated task and thus might not be a suitable application for this
particular tool.
Have you tried using genconf instead? With genconf you can easily build a
lattice of NO3 that you can then equilibrate; genbox will try to randomize the
configuration, but you can do it yourself with sufficient equilibration anyway.
-Justin
Thanks,
Adama
Adama Tandia, Corning INC, SP-TD-01-01 Corning NY 14831 USA, Tel: 607
248 1036 -GoogleVoice: 708 433 9430
--
========================================
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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