Re: Re: ABF - restricting reaction coordinate

From: Jerome Henin (jhenin_at_cmm.chem.upenn.edu)
Date: Fri Dec 07 2007 - 10:43:49 CST

Dear Vaithee,
I am correcting this in the user's guide right away.
Best,
Jerome

On Dec 7, 2007 10:38 AM, Subramanian Vaitheeswaran <vaithee_at_umd.edu> wrote:
> I just checked the log file - the default for forceConst is 0, not 10 kcal/mol/^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/^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
>
>

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