[gmx-users] FEP w/ PME inner loops
David L. Bostick
dbostick at physics.unc.edu
Tue Aug 30 20:43:04 CEST 2005
Thanks, I'll keep an eye on the gmx-revision list.
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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 Tue, 30 Aug 2005, Erik Lindahl wrote:
> Hi David,
>
> We found a couple of last minute showstoppers/failed tests, so
> hopefully later today :-)
>
> Cheers,
>
> Erik
>
> On Aug 29, 2005, at 11:15 PM, David L. Bostick wrote:
>
> >
> >
> > 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
> > =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
> > =-=-=-=-
> >
> > 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
> >>>>> =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
> >>>>> =-=-=-=-=-
> >>>>> _______________________________________________
> >>>>> gmx-users mailing list
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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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> >>
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