Mark Abraham wrote:
Dilraj Lama wrote:
Hello gmx users,
I want to perform a simulation study of a peptide
solvated
in methanol using Gromacs 3.2.1 package with gromos96 43a1
forcefiled.For the purpose I choose the "methanol.itp" for
the parameters of methanol.I am using the
"methanol216.gro" contributed by Bert de Groot.
I have set up system with the peptide solvated in a
cubic methanol box.The density of the sysytem is now
reported to be about 764.677 g/l.My query is, is it
ok for me to perform the simulation with the
mentioned density??
We don't know. Possibly this is a reasonable density for this
computational model of methanol. You need to follow a reasonable
equilibration regime, such as you have read about in the literature for
such simulations, or as here
http://wiki.gromacs.org/index.php/Steps_to_Perform_a_Simulation
and read the literature!
Mark
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--
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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