[gmx-users] g_dist

[chris.neale at utoronto.ca]

Dear Nilesh:

You don't seem to have made any progress since Mark gave you some  
reading hints. Your best chance to get a useful response follows the  
general form:

1. I want to do A.
2. I tried method B, here are the exact commands that I used (copy and paste)
3. With that method, I obtain C
4. But I am confused about why C does not look like D.
5. What is the problem?

Basically, it helps to show that you are doing your own work too.

For example, try a command on a single frame and then look at that  
frame with VMD and count for yourself and verify the answer that way.

Chris.

-- original message --

I have a system with 128 emi (cations) and 128 Cl (anions).

I want to calculate how many CL atoms are in cutoff distance relative to
hydorgen aotm of cation.  I considered all CL atoms are distinguishable.

Basically I want to calcualte the distance between each CL atom and
correponing hydorgen and registered those CL atoms which are whthin
cutoff.

How can I do ?

I am using Gromacs 4.0.7 version.

Thanks

Nilesh