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

[Erik Lindahl]

HI Yannis,

The topology looks perfect. To be more in line with standard
PDB naming, I would suggest slightly different hydrogen names though:

HA -> HC1
HB -> HC2
HC -> HC3
H  -> HO

.. but that won't affect the results of course...

As you probably noticed, this will be significantly slower since the
atom density is now twice as high. Constraints or dummies won't help 
since the slow part is the nonbonded interaction calculation.

If performance is important, you might want to try united-atom OPLS,
but that's not included in Gromacs (yet), so then you'll have to hack
some parameters yourself. Drop me a line if you want the original OPLS
parameter files.

Cheers,

Erik