[gmx-users] NVT

Dallas B. Warren Dallas.Warren at vcp.monash.edu.au
Thu Dec 1 04:17:03 CET 2005

> When I use genbox to insert 1 methane, it seems ok, but if 4 
> methane added in the following way
> Genbox  -cs  water.gro  -ci    methane.pdb -nmol 4 -box 2 2 2 
> -o out.gro

I haven't used genbox for awhile to add multiple molecules, but when I
did try to a couple of years ago that molecules would end up overlapping
and you could not minimise it.  No idea if that issue has been solved
yet or not, but by the sound of it, it hasn't.

You are best off using something like genconf.

I now use a script written by someone here, it places things much
better, rotating over three axes etc.
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.

More information about the gromacs.org_gmx-users mailing list