Re: ABF calculation using RMSD

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Mon Apr 25 2011 - 22:26:54 CDT

Hello Maiti, that depends entirely on your system. If you haven't sampled
any RMSD value higher than 21 perhaps the free energy to get there is too
high? Your samples go down gradually to zero, which suggests that high RMSD
configurations become more and more unfavorable, until maybe they're simply
forbidden. Another explanation is that some transitions that can alter the
shape of your molecular system are too slow, and you get stuck at lower RMSD
unless you add additional variables? Or alternatively, these transitions
involve going transiently to a lower RMSD, which you forbid by setting a
lower boundary very close, especially with a gigantic force constant such as
200 kcal/mol/^2.

Giacomo

---- ----
  Giacomo Fiorin - Postdoctoral Researcher
  ICMS - Institute for Computational Molecular Science - Temple University
  1900 N 12 th Street, Philadelphia, PA 19122
  giacomo.fiorin_at_temple.edu
---- ----

On Mon, Apr 25, 2011 at 11:14 PM, Buddhadev Maiti <chebm_at_langate.gsu.edu>wrote:

> Dear NAMD Users,
> I am performing ABF calculation using RMSD as a collective variable. I am
> using NAMD-2.7 version. My Distance.in file is in below. After running 4ns,
> it didn't sample lower part of window. I am sending prod.count values from
> my last window. Could anybody can suggest me about this problem, it will be
> great help for me.
> Have a nice day,
> Thanks,
> Maiti
>
> Distance.in
> Colvarstrajfrequency 1000
> Colvarsrestartfrequency 1000
> colvar {
> name GRrmsd
> width 0.1
> lowerboundary 19.780
> upperboundary 21.780
> lowerwallconstant 200.0
> upperwallconstant 200.0
> rmsd {
> atoms {
> atomsFile 1.pdb
> atomsCol O
> atomsColValue 1.0
> }
> refPositionsFile ep.pdb
> refPositionsCol O
> refPositionsColValue 1.0
> }
> }
> abf {
> colvars GRrmsd
> fullSamples 2000
> }
>
> prod.count:
> # 1
> # 19.78 0.1 20 0
>
> 19.83 1244743
> 19.93 412417
> 20.03 158821
> 20.13 57458
> 20.23 7882
> 20.33 10733
> 20.43 11685
> 20.53 2906
> 20.63 6273
> 20.73 4851
> 20.83 2651
> 20.93 2445
> 21.03 0
> 21.13 0
> 21.23 0
> 21.33 0
> 21.43 0
> 21.53 0
> 21.63 0
> 21.73 0
>
>

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