Hi Francesco,
That helps much. I am only interested in paramfit, so that the second
> option is what I want. However, is it any configuration to parallelize
> paramfit on more that two processors?
OpenMP will automatically set the number of threads equal to the number of
processors- the output I listed just said 2 as an example. If you wish to
manually set the number of threads, export OMP_NUM_THREADS=*n* where n is
the integer number of threads to use.
More importantly, is it any hope to adjust vdw params for atoms that
> are not comprised in antechamber? I mean that I plan to choose by
> intuition such params and hope that paramfit will correct them
> appropriately.
Paramfit only fits bonded forces, and does not change any nonbonded
parameters (vdw, hbonds, etc). I'm not too familiar with how to calculate
nonbonded parameters, but there seem to be a couple previous threads that
can help:
http://ambermd.org/Questions/vdw.html
http://archive.ambermd.org/200504/0376.html
http://archive.ambermd.org/201107/0357.html
Hope this helps,
Robin Betz
On Mon, Apr 16, 2012 at 10:28 PM, Francesco Pietra <chiendarret.gmail.com>wrote:
> Hi Robin:
> That helps much. I am only interested in paramfit, so that the second
> option is what I want. However, is it any configuration to parallelize
> paramfit on more that two processors?
>
> More importantly, is it any hope to adjust vdw params for atoms that
> are not comprised in antechamber? I mean that I plan to choose by
> intuition such params and hope that paramfit will correct them
> appropriately.
>
> thanks
>
> (rbetz.ucsd is not recognized by my provider)
>
> francesco pietra
>
> On Tue, Apr 17, 2012 at 12:13 AM, Robin Betz <rbetz.ucsd.edu> wrote:
> > Hi Francesco,
> >
> > You need to re-run the configure script in $AMBERHOME with the -openmp
> > option:
> > $AMBERHOME/configure -openmp gnu (or intel if you are using those
> > compilers).
> >
> > To only recompile paramfit with the openmp, go to
> > $AMBERHOME/AmberTools/src/paramfit
> > and run make install
> > Paramfit's header message will have a line saying something like:
> >
> >
> *************************************************************************************
> > Execution started at:
> > | Mon Apr 16 15:11:56 2012
> > |
> > | Running OpenMP version of code using 2 processors
> >
> > if it has been compiled correctly with OpenMP support.
> >
> > Hope this helps,
> >
> > Robin Betz
> >
> >
> >
> >
> >
> > On Mon, Apr 16, 2012 at 12:47 AM, Francesco Pietra <
> chiendarret.gmail.com>wrote:
> >
> >> Hello:
> >> I have installed without errors (after commenting out line 450 of
> >> "configure2" as Prof Case suggested)
> >> serial-ambertools12/serial-amber10 in Debian amd64 in a game machine
> >> with six CPU's and two GTX-580 cards. I would be much interested in
> >> having "paramfit" parallelized. I have an installation of OpenMPI.
> >>
> >> It is not clear to me when and where "Enable this by adding the
> >> -openmp option to configure and rebuilding paramfit" should be done. I
> >> can imagine on this particular code within ambertools12,nonetheless a
> >> bit of guideline would be helpful.
> >>
> >> Thanks
> >>
> >> francesco pietra
> >>
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> >>
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Received on Mon Apr 16 2012 - 23:30:03 PDT
