Fwd: force constant in abf configuration file

From: Madhurima Jana (tinni.217_at_gmail.com)
Date: Thu Dec 17 2009 - 11:29:50 CST

---------- Forwarded message ----------
From: Madhurima Jana <tinni.217_at_gmail.com>
Date: Wed, Dec 16, 2009 at 10:31 AM
Subject: namd-l: force constant in abf configuration file
To: namd-l_at_ks.uiuc.edu


Can anyone please explain what is the significance of the key word "abf
forceConst" in the conf file ? It is written in the NAMD tutorial that it is
"a harmonic bias is enforced at the borders of the reaction coordinate,
i.e.at both xiMin and xiMax, to guarantee that sampling will be confined
between these two values." Now when I apply this to my system it is seen
that for the change of forceconstant the number of sampling is also changing
and so the dG value for the particular value of xiMin and xiMax. In some
region no sampling is occurring on increment of force constant value also.
So how it be possible to know the particular force constant for that region


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