Re: questions regarding output data of an ABF simulation

From: Anahita Tafvizi (
Date: Mon Aug 07 2006 - 17:52:11 CDT

Dear Jerome,

Thanks a lot for your reply.

I have already tried bins of width .1 and I still don't have any thing in my
history file. from what I understand, Xi is the distance between the center
of masses two groups of atoms that I defined in my abf1 and abf2. correct?
and it's decreasing which is what i can also see in vmd since the protein is
moving toward the last base pair of DNA. but what I'm looking for is some
data for the free energy and force which is supposedly in the history file,
and that's all zero.

Thanks again,


On 8/7/06, Jerome Henin <> wrote:
> Dear Anahita,
> I see from you config file that you have setup a broad reaction coordinate
> interval with very fine bins (.01 Angstroms!), so unless you run an
> extremely
> long simulation, it is not surprising that many of these bins end up being
> empty.
> The best way to see what happens is to use the output of "writeXiFreq" and
> look at the xi(t) graph. The simplest way to do it is:
> grep "Xi at timestep" abf-run.out | awk '{print $6, $8}' > xi_of_t.dat
> and then open xi_of_t.dat with a plotting/spreadsheet program.
> At the xi positions that the system actually visits, you should definitely
> have *some* data.
> In general, a bin width of .1 Angstrom is narrow enough to describe most
> PMFs
> accurately.
> Please post back to this list any further problems you may encounter with
> ABF.
> Best,
> Jerome
> On Monday 07 August 2006 16:27, Anahita Tafvizi wrote:
> > Dear fellow NAMDers,
> > I'm seeking your help regarding a PMF calculation in NAMD using ABF.
> >
> >
> > I am trying to run ABF for lacI protein sliding along the DNA. I define
> my
> > abf1 and abf2 as the last pair of DNA and the protein respectively. the
> > last pair of DNA is completely fixed (occupancy= 100.0), and the
> backbone
> > of the rest of the DNA is also fixed but with a smaller occupancy (5.0).
> > The protein is moving toward the last pair as I want, but I don't have
> any
> > useful output data. I mean I can see the movie, but I my history file is
> > just containing zeros.
> >
> > I've attached my namd file.
> >
> > Thanks a lot in advance for your replies.
> >
> > Best regards,
> > Anahita

Anahita Tafvizi
Physics Department
Harvard University
Jefferson 262
17 Oxford Street
Cambridge, MA 02138

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