AMBER Archive (2008)

Subject: Re: AMBER: About RAMD

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Sat Jan 05 2008 - 11:47:33 CST

All: what Francesco is trying to ask (I think) is that since he HAS a
licensed version of amber9, but RAMD works with amber 8 only (for
reasons that escape me, it should be an almost trivial change in code),
can he GET a version of amber 8 without paying again ?.

Francesco, if this is what you want to do, just email me and we try to
figure it out.

Adrian

Robert Duke wrote:
> Well, Rebecca Wade does have a patch for 8, and it is on OUR web page (amber.scripps.edu; do a find on wade); maybe that's not quite standard amber, but it is some level of endorsement I would think... ;-)
> Regards - Bob Duke
> ----- Original Message -----
> From: Carlos Simmerling
> To: amber_at_scripps.edu
> Sent: Saturday, January 05, 2008 11:46 AM
> Subject: Re: AMBER: About RAMD
>
>
> I don't think that method ever made it to standard Amber.
> you will need to ask the author for the code, although I am
> not sure if she is allowed to distribute it or not.
>
> you can certainly install more than one version of Amber
> on the same machine. just check your path settings when
> you try to run a simulation.
>
>
> On Jan 5, 2008 11:26 AM, Francesco Pietra <chiendarret_at_yahoo.com > wrote:
>
> RAMD = Random Acceleration Molecular Dynamics
> http://projects.villa-bosch.de/mcm/software/amber
> Cheers
> francesco
>
>
> --- Carlos Simmerling <carlos.simmerling_at_gmail.com > wrote:
>
> > what is RAMD? do you mean REMD? if so, that is available
> > in Amber9.
> >
> >
> > On Jan 5, 2008 5:39 AM, Francesco Pietra <chiendarret_at_yahoo.com > wrote:
> >
> > > I was just informed from Professor Wade that RAMD at the moment can only
> > > be
> > > implemented into Amber 8.
> > >
> > > As I am most curious to try to follow the path of a ligand out of a
> > > protein
> > > embedded in a membrane, is it possible to get Amber 8 (having a personal
> > > license for Amber 9) and temporarily, for that computation, install it on
> > > the
> > > same machine (dual opterons, shared memory) without unistalling Amber 9?
> > > Amber
> > > 9 was ifort/icc compiled, parallel support from OpenMPI 1.2.3.
> > >
> > > Thanks
> > >
> > > francesco pietra
> > >
> > >
> > >
> > >
> >
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> >
> > 

-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu
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