[gmx-users] Re: question about force field parameter
tsjerkw at gmail.com
Mon May 25 08:24:53 CEST 2009
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.
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.
> #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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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
3584 CH Utrecht
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