Hi All,
I originally added nebrms to calcuate the RMS for energy
minimization during neb calculations. There are reduced degrees of freedom
because the atoms in the first and last image are frozen. This was a
report item that was helpful for debugging with small systems. For large
systems, it did not seem particularly important. That means that it can
now be removed unless somebody objects. I can probably help with that
cleanup next week. Hope this helps.
Sincerely,
Dave
At 08:46 PM 10/18/2007, Carlos Simmerling wrote:
>I've also sent out requests for info on nebrms, several times, with no reply.
>I'm tempted to remove all of this code if nobody owns it or knows why
>it is there.
>carlos
>
>On 10/18/07, Scott Brozell <sbrozell.scripps.edu> wrote:
> > Hi,
> >
> > sander.MPI fails to build with configure -lam g95
> >
> > mpif77 -c -O3 -fno-second-underscore -march=nocona -ffree-form -o
> force.o _force.f
> > In file _force.f:2041
> > call mpi_reduce(nebrms,etmp,1,MPI_DOUBLE_PRECISION, &
> > 1
> > Error: Symbol 'nebrms' at (1) is defined in multiple modules
> >
> >
> > Those modules are nebmodule and pimd_vars.
> > The error was introduced into force.f in
> > revision 9.43
> > date: 2007/10/15 18:01:19; author: xueli; state: Exp; lines: +14 -0
> > Add XRAY Target Function and Gradient
> >
> >
> > I shall not lay my hands on this house of cards.
> > And I repeat my request for a code inspection of LES/PIMD/NEB
> > (since I do not see any evidence that previous requests were heeded).
> >
> > Scott
> >
> > ---------- Forwarded message ----------
> > Date: Tue, 18 Sep 2007 14:50:16 -0700
> > From: Scott Brozell <sbrozell.scripps.edu>
> > Subject: Re: amber-developers: neb test case
> >
> > Hi Carlos,
> >
> > I second (or third or 4th or ...) your request for someone
> > to thoroughly inspect the LES/PIMD/NEB code.
> > .
> > .
> > .
> >
>
>
>--
>===================================================================
>Carlos L. Simmerling, Ph.D.
>Associate Professor Phone: (631) 632-1336
>Center for Structural Biology Fax: (631) 632-1555
>CMM Bldg, Room G80
>Stony Brook University E-mail: carlos.simmerling.gmail.com
>Stony Brook, NY 11794-5115 Web: http://comp.chem.sunysb.edu
>===================================================================
___________________________________________________
David Mathews, MD, PhD
Assistant Professor of Biochemistry & Biophysics
and of Biostatistics & Computational Biology
University of Rochester Medical Center
Room 3-6830
601 Elmwood Avenue, Box 712
Rochester, New York 14642
http://rna.urmc.rochester.edu
Received on Sun Oct 21 2007 - 06:07:40 PDT
