Re: atom distances

From: nmichaud_at_jhu.edu
Date: Wed Jan 04 2006 - 16:49:08 CST

You can use ptraj: http://www.chpc.utah.edu/~cheatham/ptraj.html

---------------------------------------------------------------------
Naveen Michaud-Agrawal
Program in Molecular Biophysics
Johns Hopkins University
(410) 614 4435

On Wed, 4 Jan 2006, bo baker wrote:

> Hi, Pijush:
>
> Thanks for your suggestion. It sounds complicated for me. Is there a
> simple way to do so? In amber, one can do this with a simple scriple
> to extract all the distances data from the .crd file (similar to .dcd
> file in NAMD).
>
> > already. Make an indexfile with only those two atoms and then use CATDCD to
> > extract the trajectories of those two atoms,
>
> > file, and then write a couple of lines prog. either in excel or matlab to
> > find the distance between the selected atoms over time
>
> Could you give me a bit more details about the indexfile? An example
> would be very helpful.
>
> Thank you
>
> Bo
>
> On 1/4/06, Pijush Ghosh <pijush.ghosh_at_ndsu.edu> wrote:
> > Hi Bo,
> > Its not that difficult. You have your information stored in DCD fileload it in VMD, save it as pdb
> > file, and then write a couple of lines prog. either in excel or matlab to
> > find the distance between the selected atoms over time....
> > Does this work ?
> >
> > Pijush Ghosh
> > PhD Student
> > Department of Civil Engineering
> > North Dakota State University
> > Fargo. ND. 58105. USA
> > Phone:
> > 701-231-6491(Lab)
> > 701-231-4341(Res)
> >
> > -----Original Message-----
> > From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
> > Of bo baker
> > Sent: Wednesday, January 04, 2006 2:17 PM
> > To: namd-l_at_ks.uiuc.edu
> > Subject: namd-l: atom distances
> >
> > Hello, NAMD:
> >
> > I would like to exam the distances between two charged atoms from a MD
> > run. How could I do this? I have search the mail list, and not easy to
> > find the answer. The VMD can do it by pick up the two targeted atoms.
> > But how can I get the all the distance value from the trajectories?
> >
> > Thank you for your advice.
> >
> > Bo
> >
> >
> >
>

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