VMD-L Mailing List
From: Stanley, Yemin Shi (shi_yemin_at_yahoo.com)
Date: Wed Mar 19 2008 - 15:49:08 CDT
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Dear All,
Since more and more ppl are working with VMD, is there anybody thinking of build a VMD forum?
The email will fill in the mailbox all the time, and the forum is easier to retrieve information. For example, like the forum in the www.charmm.org.
Rgds
Stanley
----- Original Message ----
From: Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu>
To: "Stanley, Yemin Shi" <shi_yemin_at_yahoo.com>
Cc: vmd-l_at_ks.uiuc.edu
Sent: Tuesday, March 18, 2008 8:25:27 PM
Subject: Re: vmd-l: Display bond breaking
On Tue, 18 Mar 2008, Stanley, Yemin Shi wrote:
YS> Dear all,
dear stanley,
YS> I have a question on the displaying setting of a bond breaking
YS> procedure. Basically, I have an .xmol trajectory file. The reaction
YS> site involves an S-H and an N. The S--H bond is suppose to break up
YS> (2.18A) and H--N bond formated (1.2A) through the trajectory. This
YS> is properly displayed in Molden. When it comes to VMD, neither the
YS> S--H break nor the H--N bond form? Any suggestions pls.
use a dynamic bonds representation.
VMD was initially written for classical MD and
there you don't have to recompute the bonding info
(which makes it _much_ faster for large systems).
this topic has been discussed a lot on the mailing
list, so please also search through the list archives.
cheers,
axel.
YS>
YS> Thanks for time
YS> Stanley
YS>
YS>
YS>
-- ======================================================================= Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu Center for Molecular Modeling -- University of Pennsylvania Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323 tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425 ======================================================================= If you make something idiot-proof, the universe creates a better idiot.
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