Re: namd: ABF query

From: Peter Freddolino (
Date: Thu Mar 20 2008 - 11:16:50 CDT

Dear Gurvisha,
I don't see the attached input file, but... if sampling hasn't passed a
certain point, it's because you haven't run the simulation long enough
to reach that point. Try sampling awhile longer.
The column order, as noted by the header, is
xi A(xi) avg_force numsamples
Which column are you confused about? numsamples just indicates how many
timesteps have been recorded within the given bin.

Peter wrote:
> Dear Namd users
> I am seeking your help regarding free energy calculation in Namd using
> ABF. In the abf output .dat file, the sampling seems to stop after a
> certain point, the force becomes zero and the A(x) value remains constant
> beyond that point. Could you explain what is causing this. Has it got
> something to do with dxi? I've included the config file as well as the
> ABF output file.
> Also, i am unable to understand how to interpret abf dist file. i dont
> know what is the column next to instantaneous force for each bin between
> xiMin and xiMax.
> Best
> Gurvisha
> Gurvisha Sehgal
> LeadInvent Technologies
> Technology Business Incubation Unit(TBIU)
> IIT Delhi
> Hauz Khas, New Delhi 110 016

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