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 Wed Jul 20 2011 - 06:30:22 PDT
