[gmx-users] Regarding g_sham

Naba nabajyoti.goswami at gmail.com
Tue Aug 4 07:37:10 CEST 2015

Dear All,
I searched a lot more things about g_sham in the mailing list and
eventually getting confused with the inputs. Just make me clear about:

1. Is it feasible to obtain free energy landscape (FEL) from a 2D
projection (using g_anaeig) of  index groups (say some loop's atoms) which
are used for the least squares fit in g_covar and then selecting index
group of elements that corresponds to the eigenvectors (say Prot-masses)?
Should I calculate covariance (g_covar) of my concerned loops separately
and then should I go for g_sham?

2. Is there any representative way to get the exact time point for the
corresponding minima obtained from g_sham?

Thanks for all previous helps...

Nabajyoti Goswami

Department of Animal Biotechnology
College of Veterinary Science
Assam Agricultural University
Khanapara, Guwahati 781022
Assam, India

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