[gmx-users] FEP w/ PME inner loops

[David L. Bostick]

Thanks Erik!

I'll check it out in a few days!

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, 29 Aug 2005, Erik Lindahl wrote:

> Hi David,
>
> Try checking out the latest CVS, which has  direct-space interactions
> with correct PME corrections.
>
> Or actually, please hold off until tomorrow since I'm hours away from
> finally releasing the first of two real betas of 3.3!
>
> Cheers,
>
> Erik
>
>
> On Aug 17, 2005, at 9:03 PM, David L. Bostick wrote:
>
> >
> >
> > 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
> > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
> > =-=-=-=-
> >
> > 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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> >>> gmx-users at gromacs.org
> >>> http://www.gromacs.org/mailman/listinfo/gmx-users
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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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> >>
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