[gmx-users] Segmentation Fault (Address not mapped)

Dallas B. Warren Dallas.Warren at pharm.monash.edu.au
Thu Aug 6 05:03:38 CEST 2009

> You indicate that I need to read the primary literature for the force
> fields. Could you please tell me where this literature can be found? I
> have searched using Google for the forcefields available for use in
> GROMACS (G43b1, G43a1, G43a2, G45a3, G53a5, G53a6, gmx), but have not
> found any primary literature for these force fields.

Google |=| primary literature

Use whatever journal search software your institution has, such as
SciFinder, and look there.  Some of the original papers are referenced
in the manual too, I think.
> With regard to your comment about demonstrating that this force field
> doing a good job at representing ammonia in the gas phase, how can I
> determine the diffusion of the pure ammonia gas? And what exactly do

There is an appendix in the manual, lists all the scripts with GROMACS
and what they can do.  Have a browse through that.  g_msd will do the
job here.

> define in my .gro file, is it not? Also, the graphene is in an ammonia
> vapour, not in a vacuum, and the graphene structure is not infinite
> has dimensions that fit well inside the simulation box. How would I
> determine if my graphene structure is stable?

Run a simulation of the graphene and see if it does anything "strange".
You noted previously that it curled up, well, that is strange.

And your graphene has to be infinite, otherwise, by definition, it isn't
graphene.  Something in the same class, which has n rings in the
molecule.  To handle graphene correctly you have to set it up so that it
repeats across the PBC, like people set up with carbon nanotubes.

Catch ya,

Dr. Dallas Warren
Department of Pharmaceutical Biology 
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

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