From: Wei Chen (gtg553p_at_mail.gatech.edu)
Date: Tue Jul 26 2005 - 17:05:39 CDT
I didn't notice that before. But I think the order is important. I guess
namd reads pdb files in for strings and then transfers different regions into
Does anybody have comments on this?
Quoting Deborah Jameson <debyjameson_at_yahoo.com>:
> Dear Wei
> I noticed the the function of B colomn, but what I mentioned is that the
> space number between two colomns interfere in the results which are given in
> fepout file. for example if you transfer all data in a colomn by one or two
> space to right or left then you will see that the results differ.
> This means that fep file should follow a specific order so that the results
> be reliable.
> this holds also when moving the minus sign by one space and the results
> change very much.
> Thanks again
> Best Regards,
> Wei Chen <gtg553p_at_mail.gatech.edu> wrote:
> Hi, Deborah,
> I don't understand what exactly you mean. Because we use B colomn to
> indicate status of each atom (fepCol B), A value of -1 in B column indicates
> the atom will vanish during the FEP calculation, whereas a value of 1
> that the atom will grow and 0 means invariant. According your needs, you
> can set those values.
> Quoting Deborah Jameson :
> > Hi Wei
> > I really appreciate your giving useful instructions and also the files
> > helped me very much in preparing my model.I could build the psf,pdf conf
> > fep files for zero-sum ethane to ethane which is mentioned in fep manual.
> > after running the model,I found out that the results are very sensitive to
> > the positions of colomns of data in fep file(specially the B colomn) and
> > results vary very much with changing the position of this colomn or other
> > colomns or even one data(e.g. -1 in B colomn).
> > I am really uncertain about the results and want to ask if you know how it
> > possible to be sure about the validity of the results.
> > I have attached the files. would you please take a look at them and check
> > significantly the results will change by changing the positions of data in
> > fep file.(for example just moving -1 in B colomn or just moving U colomn).
> > have you faced this problem yet? it is really dangerous to rely upon the
> > results when they change with simple changes in the data positions in fep
> > file.(in the manual the results are given which are different from mine)
> > Thank you very much for your consideration again
> > Best Wishes
> > Deb
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