From: Jerome Henin (jhenin_at_vitae.cmm.upenn.edu)
Date: Mon Aug 07 2006 - 18:50:20 CDT
Could you send me a compressed output file?
Jerome
On Monday 07 August 2006 18:52, Anahita Tafvizi wrote:
> 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,
>
> Best,
> Anahita
>
> On 8/7/06, Jerome Henin <jhenin_at_vitae.cmm.upenn.edu> 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
>
> --
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