[gmx-users] D value

[Dallas Warren]

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