[gmx-users] query regarding methanol density

[Mark Abraham]

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

Mark