From: bo baker (bo.bybaker_at_gmail.com)
Date: Wed Jan 04 2006 - 15:22:59 CST
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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