[gmx-users] g_sas

Dinesh Pinisetty dpinis1 at lsu.edu
Tue Mar 1 23:55:49 CET 2005

Dear Dr.Dallas,
        I got your point.I just have three more questions.
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.
2)How to determine the orientation of water dipole in lipid/water
simulation?With what command and what options?
3)How to determine mass density of alcohol in lipid/water/alcohol system?I
mean by what command?
    I appreciate your suggestions,Thanks a lot.
Thanking you,
Yours sincerely,

From:gmx-users-bounces at gromacs.org on 03/02/2005 09:35 AM ZE11

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cc:   (bcc: Dinesh Pinisetty/dpinis1/LSU)

Subject:    Re: [gmx-users] g_sas

          Actually I need the to figure out the change of the area by DPPC
lipid with respect to time.
  At the end of the simulation we can figure out the area as x*y/no.of
lipids.But I need this area change all thorugh the simulation.I  have
started the simulation with area of 0.625n m^2,I need the change in that
value all thorugh the simulation.
You want the area per lipid molecule in the bilayer?  That is typically
calculated as you noted above, so simply use g_energy to output the x and y
dimensions with time.

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
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