Re: ABF in various simulations

From: Robert Elder (rmelder_at_gmail.com)
Date: Mon May 17 2010 - 18:43:41 CDT

Unfortunately, I haven't worked much with this technique. Perhaps someone
else on the list can be more helpful.

Cheers

On Mon, May 17, 2010 at 2:18 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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