[gmx-users] D value

Dinesh Pinisetty dpinis1 at lsu.edu
Tue Mar 22 01:22:15 CET 2005

Thanks a lot Dr. Dallas Warren for your reply.I will try.
Thanking you,

From:gmx-users-bounces at gromacs.org on 03/22/2005 10:53 AM ZE11

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Subject:    Re: [gmx-users] D value

Your GROMACS manual is your friend :-)

I had no idea how you would exactly do this, just from using all the
scripts are reading through the manual (appendix E), so I then simply
looked through the manual and found the answers below ....

        Thanks a lot for your reply.But how to calculate the number of A
molecules present in the bilayer.By simple visualization it is very
difficult I guess.Is there any GROMACS command which gives us the number of
A molecules present within the bilayer.
g_dist should be able to do it, though not sure about how usable the output
is, will have to create an index file from that I think.

The other option is trjorder, since it is used for "analysing the n waters
closest to a protein".

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 9574
When the only tool you own is a hammer, every problem begins to resemble a
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