Can you actually do that or are you off by the 1 time step as usual due to
leapfrog? This appears to still be the case with amdlog files too.
I would likely accept the argument that the difference is below statistical
error, but the imin = 5 solution is guaranteed to be correct and not
particularly expensive, especially if your print step is 10^3-10^4 times
larger than your time step.
Brian
On Mon, Mar 30, 2015 at 10:34 AM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Mon, Mar 30, 2015 at 8:39 AM, Wang Moye <wangmoye13.mails.ucas.ac.cn>
> wrote:
>
> >
> >
> > Hello everyone!
> >
> >
> > I have a REMD process using AMBER12. There are 26 replicas in my system.
> > As the tutorial said, a typical use of REMD is to obtain thermodynamic
> > ensembles at temperatures of interest (e.g. 300 K). So I extracted the
> > data for each temperature . Now I want to get the potential energy for
> > each temperatue , what should I do next ? I have 26 mdcrd trajectories
> and
> > the process_mdout.perl can analyse the mdout files only.
> > If I want to get the total energy and potential energy through mdcrd
> > trajectories , which tool should I use ?
> >
>
> In addition to what Christina suggested, you can also extract the energies
> directly from the remlog files. I'm not sure if cpptraj does this (I know
> it reads remlogs, but I'm not sure if it will extract the energies into a
> data set... you could always try it and see what the manual says about it).
>
> If you plan on using cpptraj, I suggest updating to the latest version of
> AmberTools 14, as there have been numerous cpptraj improvements since Amber
> 12.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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 Thu Apr 02 2015 - 12:30:02 PDT
