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<blockquote type=cite class=cite cite>1) What option gives us x&y
dimensions in g_energy.<br>
g_energy -f ener.edr -s topol.tpr and what more option gives us the
box<br>
vectors in x& y directions for every time frame.</blockquote><br>
Look for the Box-X and Box-Y options when you run g_energy when it askes
you to select the terms for output.<br><br>
<blockquote type=cite class=cite cite>2)How to determine the orientation
of water dipole in lipid/water<br>
simulation?With what command and what options?</blockquote><br>
Don't know as not sure exactly what you want to get out of it, possibly
g_dipole or g_h2order.<br><br>
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.<br><br>
<blockquote type=cite class=cite cite>3)How to determine mass density of
alcohol in lipid/water/alcohol system?I<br>
mean by what command?</blockquote><br>
May be g_density.<br><br>
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.<br><br>
Catch ya,<br>
<x-sigsep><p></x-sigsep>
<b>Dr. Dallas Warren<br>
</b><i>Lecturer<br>
</i>Department of Pharmaceutical Biology and Pharmacology<br>
Victorian College of Pharmacy, Monash University<br>
381 Royal Parade, Parkville VIC 3010<br>
<font color="#0000FF"><u>dallas.warren@vcp.monash.edu.au<br>
</u></font>+61 3 9903 9083<br>
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