periodic boundary conditions

From: Sridhar Vaddadi (
Date: Wed Sep 30 2009 - 14:08:31 CDT

Dear Community,
I am planning to run a minization and equlibrization simulation on protein in water system. While using periodic boundary conditions, I am not sure how to assign cellbasis vectors and how to find them from my solvation pdb and psf files. Please reply me at your earliest convenience.
Sridhar Vaddadi


From: on behalf of Jerome Henin
Sent: Wed 9/30/2009 4:42 AM
To: Giovanni Bellesia
Subject: Re: namd-l: ABF calculation - normalization of the PMF

Hi Giovanni,
In short, the normalization should ensure that the PMF plateaus at
long distances, but it is still calculated up to an additive constant.
The integration procedure might use the convention that the global
minimum has zero free energy, in which case it is necessary to shift
it to get zero at large separation.

2009/9/29 Giovanni Bellesia <>:
> Hi Jerome,
> thanks for your reply.
> I am aware of the JACS paper and I will certainly use Equation 3 to
> calculate the dimerization free energy.
> However, my problem right now is with the larger values of the reaction
> coordinate: the free energy profile is
> flat but it does not "converge" to zero.
> In more details, I have two free energy profiles calculated from two
> independent simulations starting from two
> different stable conformations of the peptide dimer (see Biophysical Journal
> 96(3), 875-886 (2009)).
> The idea is to compare the two curves and check the relative stability of
> the two dimers.
> As far as I understand, to make the comparison I should "normalize" the two
> curves so that they both ==> 0 when
> the reaction coordinate is large (and the profile is flat).
> The normalization procedure in JCP 121(7), 2904 (2004) for some reason
> "works" only for one of the two curves.
> Alternatively I was thinking about simply calculate (for both curves) the
> average value of the free energy within the flat (right) section of the
> profile and then shift the curves accordingly.
> Is this correct ?
> Best
> Giovanni
> Hi Giovanni,
> To get the dimerization free energy, you'll need an integral over the
> domain of the pmf corresponding to the dimer. There is an example
> there:
> although Equation (3) in there is missing a factor 2 to account for
> the symmetry of the homodimer (see ref. 50 in that paper).
> Jerome
> 2009/9/19 Giovanni Bellesia <>:
> Hi all,
> I am trying to calculate the dimerization free energy of a short peptide
> using the ABF method.
> My 'reaction coordinate' is the COM-distance between the two peptides.
> I'm currently going through the JCP papers where the ABF method is
> introduced and evaluated.
> In particular, reading about the implementation of the method in JCP 121(7),
> 2904 (2004) I found at
> the end of Section IIB2 the comment about the normalization of the PMF via
> subtraction of the
> "Jacobian correction" from the free energy profile.
> Here's my question (just to be sure I understood correctly):
> Shall I subtract from the free energy profile the quantity
> k_B * T * ln |J|
> with |J| defined as in formula (16) ?
> Thanks for your help
> Best
> Giovanni
> --
> ------------------------------------------
> Giovanni Bellesia
> Department of Chemistry and Biochemistry
> University of California, Santa Barbara
> Santa Barbara, California 93106-9510, USA.
> Email:
> Phone: 805 893 2767
> Web:
> ------------------------------------------

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