[gmx-users] Re: question about force field parameter
zlni at u.washington.edu
Sun May 24 17:58:27 CEST 2009
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.
#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
> Message: 5
> Date: Sun, 24 May 2009 16:42:35 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] question about force field parameter
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4A18EC5B.6060707 at 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
> 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.
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