[gmx-users] NORMAL MODES analysis to compute specific heats

[Juan José Galano Frutos]

Hi there:

I've been googled a bit about this issue (
http://thread.gmane.org/gmane.science.biology.gromacs.user/49139,
http://www.gromacs.org/Documentation/How-tos/Normal_Mode_Analysis,
https://groups.google.com/forum/#!topic/archive-gmx-users/5C5Q8m9X21g), but
I've not found answers to my doubts yet.

My situation is that I want to obtain specific heats (Cp) of my systems
(protein solvated and neutralized) but, of course, at the Temperature and
Pressure of my experiments. So, my idea here is carry out a Normal Modes
analysis to extract the Hessian matrix but at least after the equilibration
step of my system. I'm interested in doing it so because Cp values only
make sense in relation with Temperature.
My doubts come up, however, when I read through the posted discussion and I
find that NM analyses apparently should be performed after minimization
steps (Conjugate gradient and/or L-BFGS). Then, I would like to ask you if
that is really so or if it is possible carry out this calculation after,
for instance, an equilibration or a productive step in which, of course,
some previous minimizations have already been performed as usual?

I've not understood also the suggestion made in one of the above referenced
discussions in which David Van der Spoel recommended set all cut-offs to
zero (=infinite), see below:

>     You can use the g96 coordinate format instead of using the trr file
>     from the conjugate gradients energy minimization.
>     Set all cut-offs to zero (= infinite).

What's the reason for that?
Where one should set to zero the cut-offs...? Just in the NM step or
that is for the minimization steps?

Thank you very much for your help.



Juan José Galano Frutos

Department of Biochemistry and
Molecular and Cellular Biology,
Faculty of Sciences,
University of Zaragoza
Pedro Cerbuna # 12, 50009
Zaragoza (Spain)
+34 976 76 28 06

Institute for Biocomputation and
Physics of Complex Systems (BIFI)
Mariano Esquillor, Edificio I + D - 50018
Zaragoza (Spain)