[gmx-users] LIE interaction

Cesar Lopez inmuno_cl at yahoo.com
Mon Feb 21 19:53:17 CET 2005

Thank you very much for your replay.
I agree with you that it is better if you work with the complete sistem, unfortunatly the sistem is very hugh, for that rason I tried to reduce my sistem cutting the protein (bad idea I think).
Could you give another alternative. It could be a good idea if I use freeze atoms????? If I do that, Will I need a non equilibrium dinamic????.
the value of G that I refer is the result after the use of g_lie, next to the resul appear a number like this (xxxxx), what does it mean?, sometimes appear a word (nan).
I used beta 0.01 and lamda 0.15
Thak you very much

Anton Feenstra <feenstra at few.vu.nl> wrote:
Cesar Lopez wrote:

> Dear users gromacs
> I am running a molecular simuation using a sistem between RNA polymerase and Ryfampicin, well I have cut the polymerase using only the active site where the ryfampicin dock, and then I have used the LIE mthod to calculate the free gibs energy.
> My question are:
> Why appear a simbol (nan) nera to the result of G
> What does it mean?
> sometimes appear numbers ( 22.222 for example), but when you modify the beta and alfa parameters it seems that it reduce the number.

You should be aware that some versions of Gromacs (notably, 3.1, I'm not 
sure of 3.2) have a bug in g_lie. You can use g_energy and a pocket 
calculator to do the calculations yourself, however.

I'm not sure it is sensible to use g_lie on a 'cutout' portion of you 
system, normally one would want the interaction energy between ligand 
(Ryfampicin, in this case I assume) and the rest of the system 
(RNApolymerase *and* solvent), and compare those with the interaction 
energy between ligand and solvent only (from a separate simulation of 
ligand in solvent!).

- Which 'results of G' are your referring to?
- modifying beta and alpha changes your free energy estimate, obviously. 
Which values have you used? Which changes did you see?



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