Re: namd: ABF query

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Mar 20 2008 - 11:49:33 CDT

Ah, sorry, I misread that and didn't see you were asking about the dist
file. Fortunately Jerome was more careful than me :)
Peter

Peter Freddolino wrote:
> 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.
>
> Best,
> Peter
>
> gurvisha_at_leadinvent.com 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
>> INDIA.

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