Re: ABF in various simulations

From: stefhoor (fabracht1_at_gmail.com)
Date: Mon May 17 2010 - 15:18:57 CDT

Ok, thanks. I Just didn't quite understand the (run without actual MD (zero
steps)) part. Since I set my abf parameters in a separate file Distance.in.
I would set the lowerboundary and upperboundary to the full sampling, I
mean, I would set the entire distance I would like to sample. And in the abf
section I would switch the "fullSamples 500" and "hideJacobian" part for
the "inputPrefix file1 file2 etc", is that right?
Now, as for the zero step simulation. I would submit a calculation, with the
same parameters used for all the previous calculations, but with "run 0" at
the end? Would this be a restart of the last run? I mean, would this run use
any of the "file.vel, file.coor or file.xsc" files from previous
calculations?
Could you give me an example file?
Thank you

2010/5/17 Robert Elder <rmelder_at_gmail.com>

> A PDF of the tutorial is located here:
> http://www.ks.uiuc.edu/Training/Tutorials/namd/ABF/tutorial-abf.pdf
> I found this on http://www.ks.uiuc.edu/Training/Tutorials/, under A
> Tutorial on Adaptive Biasing Force Calculations in NAMD.*
>
> *The part describing concatenating the files is on page 21-22 (I was just
> reading this earlier today).
>
> Cheers,
>
> Robert Elder
> PhD Candidate
> University of Colorado-Boulder
>
>
> On Mon, May 17, 2010 at 10:31 AM, stefhoor <fabracht1_at_gmail.com> wrote:
>
>> Could you please specify this link. I looked it up on namd's web site and
>> didn't find it.
>> Thank you
>>
>> 2010/5/17 Patrick Yee <pyee_at_nd.edu>
>>
>> Yes, this is a normal approach so long as the "windows" are not
>>> overlapping. See the tutorial files on the ABF website (there is a
>>> link on the NAMD website) for basic information on concatenating PMFs
>>> from ABF simulations
>>>
>>> On 5/17/10, stefhoor <fabracht1_at_gmail.com> wrote:
>>> > I need to calculate the free energy of dimerization using ABF. The
>>> problem
>>> > is that the cluster rules here allow me only to run 24Hs maximum
>>> simulation
>>> > time. So, what I usually do is to separate my simulations into several
>>> > different subsimulations and in the and concatenate all the files I
>>> need to
>>> > analyse. Would that be possible with ABF.
>>> > I have tried doing so by writing 5 different parameters.conf files and
>>> 5
>>> > different Distance.in files (Distance.in being the files with
>>> parameters for
>>> > the ABF).
>>> > Each of the Distance.in files covers a part of the lower and upper
>>> distance
>>> > to monitor,i.e., the first file contains the lines
>>> > lowerboundary 2.0
>>> > upperboundary 7.6
>>> > the second file
>>> > upperboundary 7.6
>>> > upperboundary 13.2
>>> > and so on and so forth.
>>> > Is that a correct approach? Or am I doing something wrong?
>>> > Thank you
>>> >
>>>
>>
>>
>

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