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

[Justin A. Lemkul]

Hassan Shallal wrote:
>  
> 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?
>  

Using special energy groups requires the use of energygrps in the .mdp file to 
collect the proper energy terms during the simulation.  If you did not do this, 
you can re-run your simulation using mdrun -rerun in conjunction with a .tpr 
file that contains the groups you want.  Otherwise, neither g_energy no g_enemat 
will produce anything like what you want; the decomposed energy terms simply do 
not exist.

> 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?

No.

> 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?
>  

Maybe.  There is no standard Gromacs tool for doing this, however.  There are 
various other programs that may be able to handle such a task, like HOLE 
(http://d2o.bioch.ox.ac.uk:38080/), cavity 
(http://eels.kuicr.kyoto-u.ac.jp/~tnemoto/crystal/cavity/index.en.html), or 
g_count (http://sbcb.bioch.ox.ac.uk/oliver/software/), but having never used the 
first two extensively, I can't attest to their applicability.  I used g_count 
with version 4.0.7, but I don't know if it's compatible with the 4.5 series.

It may be worthwhile to look through the literature here.  I'm sure there are 
others who have done such analysis and other programs that I didn't list here.

-Justin

> I would appreciate discussing the above questions and giving any hints or answers
>  
> Regards
> Hassan

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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