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

[Tsjerk Wassenaar]

Hi Johnny,

If for a dihedral the definition only lists two atoms, these signify
the central atoms with any possible substituents. I think this is
explained in Chapter 5 of the manual.

Cheers,

Tsjerk

On Sun, May 24, 2009 at 5:58 PM, Zhanglin Ni <zlni at u.washington.edu> wrote:
> 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
>>
>>
>>>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623