[gmx-users] FEP w/ PME inner loops

[David L. Bostick]

Hello,

I successfully checked out and compiled the CVS code of 2004/11/01, which
is supposed to include the PME inner loops for free energy calculations.
HOwever, when I grompp the topology with free_energy=yes, I get the
following warning:

WARNING 1 [file 15.mdp, line unknown]:
  You are using lattice sum electrostatics with free energy integration.
  This might give wrong results, since the lattice contribution to the free
  energy not calculated.

Was the warning left in the code even though the lattice contribution is
supposed to be calculated? I would appreciate any advisement. This warning
does not exist in the current cvs version, even though the inner loops are
not there.  It is replaced by a note as follows:

NOTE:
  State B has non-zero total charge: -1.000000e+00

Should I disregard these warnings and notes? I want to be sure all is well
before I start calculating things.

Thanks in advance,
David


-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
David Bostick					Office: 262 Venable Hall
Dept. of Physics and Astronomy			Phone:  (919)962-0165
Program in Molecular and Cellular Biophysics
UNC-Chapel Hill
CB #3255 Phillips Hall				dbostick at physics.unc.edu
Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick
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On Mon, 8 Aug 2005, David wrote:

> On Mon, 2005-08-08 at 12:54 -0400, David L. Bostick wrote:
> > Hello,
> >
> > Berk instructed me awhile ago that the free-energy innerloops that allow
> > for outputting dV/d(lambda) that includes the PME contribution can be found
> > in the CVS code of 2004/11/01.  I would like to check out this version of
> > the code, but I am only familiar with the regular checkout procedure of the
> > latest CVS code as outlined on the web page.  Could someone instruct me on
> > how to check out a version from a specific date? Forgive me if instructions
> > are actually on the web site ... if they are, I somehow missed them.
> man cvs says:
> cvs co -D 2004-11-01 gmx
>
> >
> > Also, given that these innerloops were discontinued in the code, there must
> > have been some problem with them.  Is there any reason for caution when
> > doing FEP with this version? I would be appreciative of any advice in using
> > this code.
>
> Erik will commit the new loops real soon now, but I don't knwo what was
> wrong with the old ones.
>
> >
> > Thanks in advance,
> > David
> >
> > -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
> > David Bostick					Office: 262 Venable Hall
> > Dept. of Physics and Astronomy			Phone:  (919)962-0165
> > Program in Molecular and Cellular Biophysics
> > UNC-Chapel Hill
> > CB #3255 Phillips Hall				dbostick at physics.unc.edu
> > Chapel Hill, NC 27599	           		http://www.unc.edu/~dbostick
> > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
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> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,          75124 Uppsala, Sweden
> phone:  46 18 471 4205          fax: 46 18 511 755
> spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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