Re: ABF in various simulations

From: Giacomo Fiorin (giacomo.fiorin_at_temple.edu)
Date: Mon May 17 2010 - 21:17:32 CDT

Hello Stefhoor, the "run 0" would only be used to initialize NAMD, read the
ABF files by inputPrefix, and merge them into a single one. Basically, NAMD
isn't invoked to continue the MD + ABF simulation at all... Instead, only
to reinitialize ABF and let it merge in the multiple grid files.
fullSamples and hideJacobian will only make sense if you continue the
simulation, but in this case, they don't matter.

Giacomo

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

On Mon, May 17, 2010 at 4:18 PM, stefhoor <fabracht1_at_gmail.com> wrote:

> 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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