[gmx-users] query regarding methanol density
David van der Spoel
spoel at xray.bmc.uu.se
Thu Aug 30 19:55:04 CEST 2007
Mark Abraham wrote:
> Dilraj Lama wrote:
>> Hello gmx users,
>> I want to perform a simulation study of a peptide
>> 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
and read the literature!
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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.
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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