Hi,
I'm wondering if there is a program in AmberTools 1.5 that is equivalent to
paramfit? Or is it necessary to install AmberTools12 in order to
parameterize bonding interactions? Thanks for the help.
Sid
On Mon, Apr 16, 2012 at 11:00 PM, Robin Betz <rbetz.ucsd.edu> wrote:
> 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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Received on Tue Apr 17 2012 - 01:00:03 PDT
