From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sat Nov 12 2011 - 01:14:09 CST
This is also covered in the appendices of the NAMD tutorial.
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf Of johan strumpfer
Sent: Friday, November 11, 2011 6:22 AM
To: Marco Sant
Cc: namd-l-digest_at_ks.uiuc.edu
Subject: Re: namd-l: improper angle
Dear Marco and Bin,
Looking at the code - the angles is between the planes 1-2-3 and 2-3-4. I presume also that when you ask about the restriction, you're referring to CHARMM-formatted parameters files for use in namd. Indeed there is a restriction, the order of the atoms must match the order they are found in the IMPROPER entry of the psf file. If I remember correctly, the convention is that the central atom is in position A in A-B-C-D.
Cheers,
Johan
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Johan Strumpfer: johanstr_at_ks.uiuc.edu www.ks.uiuc.edu/~johanstr <http://www.ks.uiuc.edu/%7Ejohanstr>
Theoretical and Computational Biophysics Group
3115 Beckman Institute
University of Illinois at Urbana-Champaign
405 N. Mathews
Urbana, IL 61801, USA
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On Fri, Nov 11, 2011 at 3:34 AM, Marco Sant <labicia_at_yahoo.it> wrote:
Dear all,
if in the parameters file I specify an improper angle
as formed by the following atoms:
A-B-C-D
does it mean that the improper angle is the one
between the planes A-B-C and B-C-D ??
I guess so looking at the meaning of dihedral angle,
A-B-C-D, as angle between planes A-B-C and B-C-D,
and seeing in the source code that dihedrals and impropers
have a similar approach.
Still, I have to answer to a referee for the publication
of an article and I need a RELIABLE answer.
I apologize if this is explained somewhere and it is
just me that cannot find it!
Secondary aspect. In an improper angle there
is always a central atom to which other three atoms
are connected.
In the lower schema the central atom is numbered as 1.
3
|
1
/ \
2 4
Is there a restriction, when I specify the potential for the
improper A-B-C-D, to which position the central atom
should have?
For example, in my calculations I specify the improper
of the above schema as: 2-3-1-4.
In other words: should the central atom 1,
appear in position B and C, or in position A and D,
when specifying A-B-C-D improper?
Thanks a lot,
Marco and Bin
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