RE: ABF question

From: jia (jia_at_ornl.gov)
Date: Sun Jan 13 2008 - 12:55:37 CST

Hi Jerome and NAMD users,

I started over with better configurations and it seems working now. However,
the new problem is that the RC is not equally sampled. I've tried with
different interval, initial configurations and bin width, and one of the
borders is always oversampled than the rest. I would greatly appreciate any
help and advice. Thanks much.

Jiancong

>===== Original Message From Jerome Henin <jhenin_at_cmm.chem.upenn.edu> =====
>Hi Jiancong,
>
>It is best to prepare an equilibrated system with the RC in the
>desired range, using any kind of appropriate restraints. The boundary
>biases of ABF are harmonic - if you start far away from the min or max
>value, the excessive pulling on the system may have side-effects.
>
>An ABF tutorial is in preparation. We will announce it on this mailing
>list when it goes online - this should not take very long.
>
>Jerome
>
>On Jan 9, 2008 11:04 AM, Xu, Jiancong <xuj1_at_ornl.gov> wrote:
>>
>> Hi All,
>>
>> I'm performing an ABF calculations with the reaction coordinate spanning
between 20 and 30 A defined by "distance-com". The reaction coordinate was
split into 2 windows (1) 20 -25 A, (2) 25-30 A. From a short simulation, about
100ps long, no single data point fell into the 25-30 A range. Does this mean
the default force constant applied at the borders of the reaction coordinate
(10 kcal/mol/A2) is too small?
>>
>> I'm also wondering if there's any ABF tutorial available on NAMD website
with all the input files for a model system. That'd be greatly helpful.
>>
>> Jiancong
>>
>>

Postdoc Research fellow
Center for Molecular Biophysics,
Oak Ridge National Lab
Oak Ridge, TN, 37830

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