Thanks very much, Dan.
Great idea, I'll try it.
Dean
On 8/14/11 2:16 AM, "Daniel Sindhikara" <sindhikara.gmail.com> wrote:
>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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>
>
>
>--
>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 Mon Aug 15 2011 - 22:00:02 PDT
