[gmx-users] generating new velocities and exploring more of thephase space

[Hassan Shallal]

Thanks a lot Justin for the valuable feedback about generating different velocities a few days ago...
 
I would like to discuss some analysis questions with the gromacs users, I tried to find solutions to the following points in the literature and/or the mailing list, unfortunately, couldn't find any..
 
1- Traget: measuring the energetics of interaction (Coulomb and LJ) between certain loops within the protein structure using g_energy or g_enemate
Plan: making index files with those specific loops and use the .ndx file to introduce these groups to the g_energy using the -n option as mentioned in one of the threads in the mailing list(http://lists.gromacs.org/pipermail/gmx-users/2008-December/038588.html)
Problem: g_energy compiled from gormacs 4.5.2 version doesn't have an option for index files!!
               g_enemate has an option for groups.dat file, when I changed my loops.ndx to loops.dat and tried 
               to use it with g_enemate, g_enemate was not able to deal with it!!
Question: Is there anyway I can get the above measurment using gromacs analytical tools?
 
2- Traget: measuring time evolution of the size of a binding pocket along the trajectory.
Approach: I was thinking that the volume of a a binding pocket between cerain loops of the studied protein can be related to the number of water molecules being able to occupy this pocket which by changing along the time trajectory can give a quantitative (yet simplified) picture about the time evolution of the volume of that pocket
Question: is there anyway to measure the size (volume) of a given binding pocket using .ndx file of the surrounding loops and a specific analysis tool in Gromacs?
Question: If the answer to the above question is no. Would my approach of measuring the number of the solvent molecules occupying this pocket make sense? and if yes, how can I do this using Gromacs analytical tools?
 
I would appreciate discussing the above questions and giving any hints or answers
 
Regards
Hassan
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