[gmx-users] box of methanol

[Erik Lindahl]

nicolis at guideo.fr wrote:

>>You don't need to know the exact compressibility, just the order of 
>>magnitude. The only place where it enters is the pressure scaling, but 
>>it only affects the speed of scaling, not the equilibrium pressure.
>>
>
>OK Erik, thanks for the answer, but in that case, there must be something I 
>am doing wrong because I don't get the right density. After 1000ps with the 
>methanol.itp of the $GMXDATA/top and the ffG43a1 forcefield, I end with a 
>density of 850 instead of 791.
>Maybe the 3x3x3 box (550 methanols) is too small?
>Thanks,
>Yiannis
>
Not sure; you should probably check the forcefield article and check 
their results - I
guess Wilfred and the gang included methanol in the tests.

Also make sure you use the right temperature and cut-off parameters. 
Ewald summation
will often give a too high density; Gromos-96 was parameterized with 
0.8/1.4 twin-range
cut-offs.

You might also want to try OPLS, but there's no methanol topology there 
yet, so it has
to be handcoded (with all dihedrals).

Cheers,

Erik