Re: ABF in various simulations

From: Robert Elder (rmelder_at_gmail.com)
Date: Mon May 17 2010 - 14:42:30 CDT

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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