Pmemd14 does TI in the same way as sander does. Both codes provide MBAR data. So one can easily compare how old a hat TI really is :-)
________________________________________
From: Brian Radak [brian.radak.accts.gmail.com]
Sent: 28 January 2015 19:15
To: AMBER Mailing List
Cc: filipfratev.yahoo.com
Subject: Re: [AMBER] FEP
That depends on what you mean by TI. As far as I know, pmemd has never
supported the dual-topology/single-coordinate simulation method that is
implemented in sander. While that (i.e. the sander code) may be the only
code that directly reports Hamiltonian derivatives, you should still be
able to recompute them as a post-processing.
Alternative estimation strategies such as MBAR are becoming increasingly
more popular anyway. TI is something of old hat these days.
Regards,
Brian
On Wed, Jan 28, 2015 at 12:56 PM, <hannes.loeffler.stfc.ac.uk> wrote:
> Yes, you are right about this.
> ________________________________________
> From: filip fratev [filipfratev.yahoo.com]
> Sent: 28 January 2015 18:12
> To: federica.chiappori.itb.cnr.it; AMBER Mailing List
> Subject: Re: [AMBER] FEP
>
> Hi Federica,>I will perform TI as explained in the amber14 reference
> manual.
> >I'm employing pmemd to perform these simulations because I'm using a GPU
> >server.
> I don't think that TI calculations are supported by the GPU version. Am I
> right?
>
> Regards,Filip
>
>
>
> On Wednesday, January 28, 2015 12:11 PM, Federica Chiappori <
> federica.chiappori.itb.cnr.it> wrote:
>
>
> Dear all, thank you for your answers and suggestions.
> Finally, I will perform TI as explained in the amber14 reference manual.
> I'm employing pmemd to perform these simulations because I'm using a GPU
> server.
> In the reference manual is described how to obtain a single topology file
> for wt and mutant proteins, but there is not described how does the group
> file looks like (pag. 351). In particular: mdin and prmtop are the same
> files for both lines and only the outputs are different, are both line
> necessary? Or with the new commands (timask and scmask) I will obtain all
> the informations in a single file?
>
> Many thanks for helping me.
>
> Federica
>
>
> On 15 January 2015 at 01:10, Jason Swails <jason.swails.gmail.com> wrote:
>
> >
> >
> > On Wed, Jan 14, 2015 at 6:24 AM, Federica Chiappori <
> > federica.chiappori.itb.cnr.it> wrote:
> >
> >> Dear Amber,
> >> I will perform a Free Energy Perturbation to evaluate the effect of a
> >> mutation. If I correctly understand the Amber module to perform FEP is
> the
> >> Gibbs module, but the last version including this module is the Amber7.
> >>
> >
> > If you can implement a mutation by creating prmtop files that
> interpolate
> > between two "end-state" prmtops, then you can run FEP calculations by
> > simulating each window directly in sander/pmemd and post-processing the
> > resulting trajectories to extract the FEP free energy (either using the
> > basic FEP equations or something a bit more sophisticated like MBAR).
> > ParmEd makes it easy to scale charges, and with a little work can
> > interpolate van der Waals parameters as well.
> >
> > You can also use the H-REMD functionality in sander/pmemd to implement
> > replica exchange free energy perturbation (REFEP). For example the
> > following H-REMD/REFEP study was carried out using this functionality
> > currently implemented in Amber:
> > http://pubs.acs.org/doi/abs/10.1021/ct200153u
> >
> > It is possible to obtain this module separately?
> >>
> >
> > As far as I understand, it would not be feasible to run GIBBS for a
> > current study now, even if someone was able to dig up the source code.
> >
> >
> >>
> >> I have Amber 12 and Amber14 available, is there any other tool to
> perform
> >>
> >> FEP?
> >>
> >
> > Outside of what I described above, no other part of Amber (that I'm
> > familiar with) supports FEP.
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> >
>
>
>
> --
> Federica Chiappori, Ph.D.
> Istituto di Tecnologie Biomediche - CNR
> Via F.lli Cervi, 93
> 20090 Segrate (MI)
> Phone: +39 02 26422606
> E-mail: federica.chiappori.itb.cnr.it
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>
>
>
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--
Brian Radak
Postdoctoral Scholar
University of Chicago
Department of Biochemistry & Molecular Biology
Gordon Center for Integrative Science, W323A
929 E. 57th St.
Chicago, IL 60637-1454
Tel: 773/834-2812
e-mail: radak.uchicago.edu
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Received on Wed Jan 28 2015 - 12:00:02 PST
