[gmx-users] g_covar + g_anaeig entropy calculation

Albert mailmd2011 at gmail.com
Thu Dec 4 14:00:31 CET 2014


I am trying to calculate ligand binding energy for  protein/ligand
system. The enthapy part was done by GMXPBSA. Now I would like to
evalutate the entropy part with g_covar + g_anaeig.

Here I got some questions:

--- is it necessary using double precison Gromacs for entropy evaluation?

--- I googled a lot concering on this topic from Gromacs mailist. If I
understand correctly, we should
(1) generate eigenvec.trr as input file for g_anaeig
(2) use g_anaeig calculate the entropy

is it correct?

---I am trying to run command:
g_covar -f input.xtc -s input.tpr -n -o eigenval.xvg -v eigenvec.trr -av
average.pdb -l covar.log -ascii covar.dat -xpm covar.xpm -xpma covara.xpm

The trajecotry I am using for above commend was extracted from MD
simulations and water/ions were removed from the system. When g_covar
pop up a dialoug asking which compoenent I am going to analyze, I
selected "System" which contains protien+ligand

Is it correct to do so?

---I am planning to run g_anaeig with following command for entropy
g_anaeig -v  eigenvec.trr -entropy  -s input.tpr  -comp

Shall I speicify additional options for this purpose?

Thank you very much.


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