[gmx-users] Wildcards and dihedral type 9

[Mark Abraham]

On 27/01/2012 8:59 PM, Mark Abraham wrote:
> On 27/01/2012 6:22 PM, Antila Hanne wrote:
>> Dear experts,
>>
>> I'm a bit confused about the use wildcards in the dihedral definitions
>> of .itp force field files. I'm under the impression that explicit
>> definition of a dihedral (e.g. OS-CT-CT-OS) is always used if
>> available and it overwrites any wildcards (for example X-CT-CT-X) that
>> might match that particular dihedral. However:
>>
>> 1. Does the explicit definition replace wildcard if they have
>> different periodicity. That is, are the expressions matched based on
>> atom types alone or atom types and periodicity?
>
> Don't know, but if you make a simple test case, you can use gmxdump to 
> see what grompp decided to do. Note that the output of gmxdump starts 
> numbering from zero, not one.

Easier still is to make a local copy of the forcefield folder, run 
grompp using the normal version. Then change one thing that will test 
the effect of the above. Re-run grompp and use gmxcheck to compare the 
"before and after" .tpr files.

Mark

>
>>
>> 2. Does the use of dihedral type 9, which enables summation of several
>> (type 1) dihedrals, have an effect on this?
>
> I doubt it.
>
> Mark
>
>>
>>   Thanks for the help!
>>
>>   Hanne Antila
>>   Phd student
>>   Aalto University
>>   Finland--
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>