AMBER Archive (2008)

Subject: Re: AMBER: About RAMD

From: Robert Duke (rduke_at_email.unc.edu)
Date: Sat Jan 05 2008 - 11:05:55 CST

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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>

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