From: Subramanian Vaitheeswaran (vaithee_at_umd.edu)
Date: Fri Dec 07 2007 - 09:38:36 CST
I just checked the log file - the default for forceConst is 0, not 10 kcal/mol/Å^2 as the user guide says!
TCL: ABF> forceConst : 0.0 [default]
Vaithee
---- Original message ----
>Date: Fri, 7 Dec 2007 09:55:48 -0500 (EST)
>From: Subramanian Vaitheeswaran <vaithee_at_umd.edu>
>Subject: ABF - restricting reaction coordinate
>To: namdlist <namd-l_at_ks.uiuc.edu>
>
>Dear Chris and Jerome,
>
>Following both your suggestions a couple of days ago, I split the range of my reaction coordinate (a dihedral angle) into four windows. I specify the following in my .conf file:
>********************************
>abf coordinate dihedral
>abf abf1 {8 6 12 16}
>abf dxi 1.0
>abf xiMin 0.5
>abf xiMax 45.5
>abf writeXiFreq 50000
>********************************
>So, I expect that xi will be in the range [0.5, 45.5] degrees for *every* step.
>
>But xi is almost never in this range - here is a small fragment grepped from the log file:
>********************************
>TCL: ABF> Xi at timestep 4300000 : -119.747074603
>TCL: ABF> Xi at timestep 4350000 : -44.6413954893
>TCL: ABF> Xi at timestep 4400000 : -55.1637937915
>TCL: ABF> Xi at timestep 4450000 : -108.865140314
>TCL: ABF> Xi at timestep 4500000 : -155.734544341
>TCL: ABF> Xi at timestep 4550000 : -57.9804339106
>TCL: ABF> Xi at timestep 4600000 : -160.710021078
>********************************
>Does this imply that the default value for forceConst of 10 kcal/mol/Å^2 is too small for this system? Do you see any problems with increasing it to an arbitrarily large value?
>
>Thanks for all your help,
>Vaithee
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:40 CST