[gmx-users] methanol/water mixture with all atoms

Dallas B. Warren Dallas.Warren at vcp.monash.edu.au
Wed Mar 1 22:32:25 CET 2006

>(1) I downloaded equilibrated methanol box (pdb) with opls from the
gromacs website
>(I need an all-atom model for MeOH).  When I pdb2gmx, I get the
following error message:

Why are you running it rhough pdb2gmx?

Is there a .itp or .top file in the zip file you downloaded?  If so,
then that is what you use.  You don't run it through pdb2gmx, that is
from taking a pdb file for proteins and generating the topology files.

>(2) What I really want is an all-atom butanol/water or methanol/water
(1:3 in mole fraction) mixture
>with about 400 molecules total. How do people usually generate initial
coordinate file for such a system?

Doesn't really matter too much, you can start with a very regular
crystal like packing, you can use the genconf script to do that, you
randomise it (but there isn't a script with GROMACS that does that very
well currently, will have to run your own or use someone else's).

>(3) Does opls/tip4p sound like a reasonable combination for the
simulation of the methanol/water system?
>If not, could you please recommend one?

Best idea is to check the literature on that one, what has been done
perviously along the lines of what you are looking to do.

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9073
When the only tool you own is a hammer, every problem begins to resemble
a nail.

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