The reason I asked the question was becuase I was trying to understand them
in order to parameterize some bonds myself.
for example, dihedral angles a lot time are clearly commented, so I know
which bonds could use the parameter.
e.g.
#define gd_4 180.000 5.86 1
; N-CHn-CHn-OA (lipid) 1.4
;
#define gd_5 180.000 9.35 1
; OA-CHn-CHn-OA (sugar) 2.2
But those like following is comfusing to me which conditions they are
discribing since it commented 2 atoms for a dihedral angle
#define gd_38 0.000 0.0 4
; -NR-FE- 0.0
;
#define gd_39 180.000 1.0 6
; -CHn-N,NE- 0.24
;
#define gd_40 0.000 1.0 6
; -CHn-C,NR(ring), CR1- 0.24
;
thanks
Johnny
Message: 5
Date: Sun, 24 May 2009 16:42:35 +1000
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] question about force field parameter
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <4a18ec5b.6060...@anu.edu.au>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Zhanglin Ni wrote:
Dear all
I am a little confused with some force field parameter library. for
example
Whether and how this makes sense depends on the context, which you need
to tell us, since we are not going to go looking and guessing for you. :-)
#define gd_26 0.000 2.93 3
This defines a preprocessor macro called gd_26 that replaces each
instance of that token string with the three numbers above.
; -CH2-S- 0.7
This is a comment line.
dihedral is supposed to be i j k l 4 atoms , why, for example, the case
above has only 2 atoms.
You may need to consider the effect of that macro in the context where
it is used.
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
