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2010/4/21 Yunfen Wang <wangfen041237.163.com>
>
>
>
> Thank you very much , Jason!
>
> as you say " I know that VMD makes it quite easy to measure dihedrals,
> distances, or angles and
> plot them as a function of time.“
>
> But I did not find the tool in VMD menu for measuring dihedrals,
> distances, or angles and
> plot them as a function of time.Could you explain it for me ?
>
>
>
> Thanks a lot !
>
> Wang
>
>
> 在2010-04-20 20:16:42，"Jason Swails" <jason.swails.gmail.com> 写道：
> >Hello,
> >
> >If you are trying to measure a particular dihedral angle as the simulation
> >progresses, you can do this with ptraj using the "dihedral" command, which
> >is clearly explained in the manual.
> >
> >Alternatives are to use molecular visualization programs, such as pymol
> and
> >VMD. I do not use pymol regularly, though I believe it can do this. I
> know
> >that VMD makes it quite easy to measure dihedrals, distances, or angles
> and
> >plot them as a function of time. If you are looking for the value of the
> >dihedral as a function of time, you do not just need the trajectory of the
> >Pr only (whatever Pr may be...). However, if you only want the Pr part,
> use
> >the strip command like Carlos suggested (which is also detailed quite
> >thoroughly in the manual). Note that if you keep it as an mdcrd or netcdf
> >file, you'll have to create a matching prmtop to make use of it.
> >
> >Good luck!
> >Jason
> >
> >On Tue, Apr 20, 2010 at 4:09 AM, Yunfen Wang <wangfen041237.163.com>
> wrote:
> >
> >> Hi all,
> >> I have done MD simulations of protein in water and got the trajectory
> file
> >> . But now , i want to analysis dihedral angel of the Pr , how can i get
> the
> >> trajectory file of pr only . Or , it just need the final structure of pr
> to
> >> analysis dihedral angel. if this is true , how to character the change
> with
> >> time? Any instruction ?
> >> Thank you !
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> >
> >
> >
> >--
> >---------------------------------------
> >Jason M. Swails
> >Quantum Theory Project,
> >University of Florida
> >Ph.D. Graduate Student
> >352-392-4032
> >_______________________________________________
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>
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Received on Wed Apr 21 2010 - 04:00:03 PDT
