Dean,
Do you expect time periodicity in your system? We typically expect
biomolecules to be chaotic and thus as long as your windowing is longer than
the inherent autocorrelation time you will have no problems. If you think
there are periodicity issues, that is a whole other problem. If you want to
randomize trajectories for some other reason, you can write a script to
write a ptraj input script to grab random frames.
e.g.
trajin mytraj.mdcrd 135 135
trajin mytraj.mdcrd 253 253
...
trajout myrandomizedtraj.mdcrd
Hope that helps.
-Dan
On Sun, Aug 14, 2011 at 9:21 AM, Tai Chi For Me <dean.taichiforme.com>wrote:
> Dear all,
>
> To avoid periodicity in my selection of frames in a trajectory, can
> someone please tell me how to randomly select frames from a trajectory and
> dump into a new trajectory, or equivalently, simply randomize an entire
> trajectory.
>
> The only thing I saw was the random variable in the sieve function of
> cluster in ptraj, but I couldn't get it work.
>
> Thanks in advance!
>
> Dean
>
>
> On 8/12/11 7:30 PM, "Jason Swails" <jason.swails.gmail.com> wrote:
>
> >There is a residue list in the topology file under RESIDUE_LABEL, or if
> >you are talking about the ones used by leap, then they are in
> >$AMBERHOME/dat/leap/lib/amino10.lib. The protonated form if ASP is ASH,
> >protonated GLU is GLH, deprotonated LYS is LYN, and deprotonated CYS is
> >CYM.
> >
> >HTH,
> >Jason
> >
> >--
> >Jason M. Swails
> >Quantum Theory Project,
> >University of Florida
> >Ph.D. Candidate
> >352-392-4032
> >
> >On Aug 12, 2011, at 6:47 PM, "E. Nihal Korkmaz" <enihalkorkmaz.gmail.com>
> >wrote:
> >
> >> Dear all,
> >>
> >> How can i find the residue list? I mean, different versions (according
> >>to
> >> protonation state) of Lys, Asp, Glu and Cys. I know the versions of His
> >>but
> >> i didn't come across anything for the other ionizable residues.
> >>
> >> Best,
> >>
> >> --
> >> Elif Nihal Korkmaz
> >>
> >> Research Assistant
> >> University of Wisconsin - Biophysics
> >> Member of Qiang Cui & Thomas Record Labs
> >> 1101 University Ave, Rm. 8359
> >> Madison, WI 53706
> >> Phone: 608-265-3644
> >> Email: korkmaz.wisc.edu
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
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--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
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Received on Sun Aug 14 2011 - 00:30:02 PDT
