[gmx-users] What if there are multi-definition of dihedrals?
leafyoung at yahoo.com
Tue Jul 17 10:15:37 CEST 2007
Entries in [ bonds ], [ pairs ], [ angles ], [ dihedrals ] are additive.
Repeat the entry for two or more times will effectively double or triple
On 7/17/2007 3:02 PM, Tsjerk Wassenaar wrote:
> Hi Wu Yanbin,
> Multiple definitions are combined. (Isn't this in the manual?)
> On 7/17/07, WU Yanbin <wuyb02 at gmail.com> wrote:
>> Hi, All,
>> If there are multi-definitions of the same dihedral in topology
>> file, how
>> will gromacs treat it? Using the second one, or the addition of the two
>> The reason for my asking this is: a dihedral potential function
>> like the
>> following needs to be realized ,
>> V = sum(Cn*cos(phi)^n), n=1, 2, 3, 4, 5, 6.
>> But the RB function in gromacs is limited for n up to 5.
>> If multi-definition is considered as addition, the potential
>> function can
>> be splitted into two, one using RB function and the other using proper
>> dihedral funciton with n=6.
>> If not, can anyone recommend one solution? Thanks.
>> Yours Sincerely,
>> WU Yanbin
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