Thank you for reply . I will grow through the mentioned literature.
On Wed, Jul 20, 2011 at 6:56 PM, Daniel Sindhikara <sindhikara.gmail.com>wrote:
> The second column is the collective variable (aka reaction coordinate). If
> you are unsure how to extract the "free energy" from an umbrella sampling
> simulation, I suggest you read some papers on it. Suffice to say you will
> need to do reweighting after obtaining sufficient sampling. I have some
> software here:
> http://www.sciencedirect.com/science/article/pii/S0010465511001640 that
> can
> help you do this.
>
> Also if your anchor position is 2 and your CV is staying around 12, there
> is
> something very wrong. Likely you have an unrealistic sense of what the CV
> should be, your anchor strength is too weak, or you need to slowly move
> your
> system to that CV value. Again, there is a plethora of umbrella sampling
> literature that will be informative on this matter.
>
> --Dan
>
> On Tue, Jul 19, 2011 at 10:00 PM, jani vinod <genomejani.gmail.com> wrote:
>
> > Dear all,
> > I have basic doubt about umbrella sampling input file with MULTI_RMSD as
> > variable type.
> > In input file what actually the *anchor position* will represent for this
> > variable type .
> > I just tried a test run for umbrella sampling for my system with *
> > anchor_strength=4
> > and anchor_postion=2*(considering this to be the RMSD with respect to
> > *reference
> > coordinate in r list*)
> > i got following output
> >
> > # = NCSU%PMD ==============================
> > ====================================
> > # << anchor(1) : position = 2.000000, strength = 4.000000 >>
> > #
> >
> >
> -----------------------------------------------------------------------------
> > # MD time (ps), CV(1:1)
> > #
> >
> >
> =============================================================================
> > 72930.0000 12.06435767
> > 72930.0200 12.06543885
> > 72930.0400 12.06576154
> > 72930.0600 12.06246635
> > 72930.0800 12.05852483
> > 72930.1000 12.05584864
> > 72930.1200 12.05587321
> > 72930.1400 12.05643840
> > 72930.1600 12.05711092
> > 72930.1800 12.05716360
> > 72930.2000 12.05681497
> > 72930.2200 12.05736231
> > 72930.2400 12.05748523
> >
> > Here what does *second column represents* . And how one should go about
> > from
> > this point to calculate free energy .
> >
> > Thanks
> > _______________________________________________
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> >
>
>
>
> --
> Dr. Daniel J. Sindhikara
> Institute for Molecular Science
> E-mail: sindhikara.gmail.com
> Website: http://sites.google.com/site/dansindhikara/
> --
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Received on Thu Jul 21 2011 - 02:30:03 PDT
