[gmx-users] Re: question about force field parameter

[Zhanglin Ni]

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.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 
>> 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
>
>
>>