[gmx-users] g_covar

[Faezeh Pousaneh]

Hi,

I need help please.
I am calculating entropy of a single water in water solution. So I did a 10
ns NPT. Then I run

g_covar -f NPT.xtc -s NPT.tpr  -o  -l   -av   -v

and

g_anaeig_d -v eigenvec.trr -entropy -eig eigenval.xvg


I have two questions.

1- In the g_covar it asks to select group,  should I choose 'system'
for both asks, or choose a 'single water'?

2- When I choose different time frames (of course after equilibrium), I get
completely different entropy, why is that so?

Best regards