[gmx-users] g_sas

Dinesh Pinisetty dpinis1 at lsu.edu
Tue Mar 1 23:23:57 CET 2005

Respected Dr.Dallas,
          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.
  Hope I was clear to you.
Thanking you,
Your sincerely,

From:gmx-users-bounces at gromacs.org on 03/02/2005 09:08 AM ZE11

Sent by: gmx-users-bounces at gromacs.org

Please respond to Discussion list for GROMACS users <gmx-users at gromacs.org>

To:   Discussion list for GROMACS users <gmx-users at gromacs.org>
cc:   (bcc: Dinesh Pinisetty/dpinis1/LSU)

Subject:    Re: [gmx-users] g_sas

   When I used g_sas -f traj.xtc -s topol.tpr -o area.xvg,I got the output
file with
  0    102.4    255.7  124   0  etc which I have no idea of.Can anyone tell
Check the header text of the any text data file generated by GROMACS, it
typically tells you there what each column is.  From memory, for g_sas
(which calculates solvent accessible surface area) it is time, hydrophobic,
hydrophilic, total and enthalpy, or some variation of that.  Check the
header text, it will tell you.

me what options should be used with g_sas to get the desired temporal
behavior of lipid.It should be of the order 0.6-0.7.
What do you mean by temporal behaviour?

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
gmx-users mailing list
gmx-users at gromacs.org
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list