[gmx-users] Re:[gmx-users] box of methanol

[nicolis at guideo.fr]

OK here are my density results on the OPLS methanol box. I need your 
opinion on that:
I tried two different boxes, both cubic, one 3x3x3 and one 5x5x5 both filled 
by genbox with the OPLS methanol topology I send a few days ago. The 
3x3x3 box equilibrates at a mean density of 759 and the 5x5x5 at a mean 
density of 807, which is closer to the real 791. Both values are better than 
the 851 I obtained with the G43a1 force field in a 3x3x3 box.

Does this mean I have to use a 5x5x5 box for my simulation or do I have to 
modify something on my cutoffs?

For both boxes I used PME but with different distance parameters.

In the 3x3x3 box I use:
rlist                    = 1.3
coulombtype              = pme
rcoulomb-switch          = 0.7
rcoulomb                 = 1.3
vdw-type                 = Cut-off
rvdw-switch              = 0.7
rvdw                     = 1.3

In the 5x5x5 box I use:
rlist                    = 2.2
coulombtype              = pme
rcoulomb-switch          = 1.2
rcoulomb                 = 2.2
vdw-type                 = Cut-off
rvdw-switch              = 1.2
rvdw                     = 2.2

Thanks for any suggestion.

Yiannis

P.S. If you think these are OK I will upload the box and the itp on the 
gromacs web topologies