[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 
>> 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.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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