[gmx-users] g_sas

Dallas Warren dallas.warren at vcp.monash.edu.au
Wed Mar 2 00:21:58 CET 2005

>1) What option gives us x&y dimensions in g_energy.
>  g_energy -f ener.edr -s topol.tpr and what more option gives us the box
>vectors in x& y directions for every time frame.

Look for the Box-X and Box-Y options when you run g_energy when it askes 
you to select the terms for output.

>2)How to determine the orientation of water dipole in lipid/water
>simulation?With what command and what options?

Don't know as not sure exactly what you want to get out of it, possibly 
g_dipole or g_h2order.

I always flick through Appendix E when I am looking to generate some data 
from a simulation.  More times than not, there is a script there that will 
do what you want it to, you just need to look.

>3)How to determine mass density of alcohol in lipid/water/alcohol system?I
>mean by what command?

May be g_density.

The documentation provided with GROMACS I think is exceptional, so look 
through the manual and use the -h switch with the various scripts to get 
more information on how to use them.  Then try it out and see if what you 
get is what you are looking for.

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 9083
When the only tool you own is a hammer, every problem begins to resemble a nail.
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