[gmx-users] Tabulated potentials for dihedrals - regd

Mark Abraham Mark.Abraham at anu.edu.au
Mon Jun 4 09:25:58 CEST 2012

On 4/06/2012 3:46 AM, ramesh cheerla wrote:
> Dear Gromacs experts,
>                                   I am planing to use tabulated 
> potentials for dihedral functional form Summn over 'n'  0.5*K [ ( Cos  
> n(phi-phi0)] , Here 1<= n <= 3 . I have three different K values (i.e 
> K1,K2,K3 ) one for each 'n' value ( Here 'n' is multiplicity).

You do not need a table for this - type 9 will do the job easily, and 
for friendly values of phi0, there exists an equivalent form to the 
above that can be expressed as a Ryckaert-Belleman dihedral. See various 
places of manual chapters 4 and 5.

>   I have generated  table and given the table number in dihedrals 
> directive of the  ffbonded.itp file, According to my understanding one 
> has to supply K ( force constant ) value in addition to table number 
> in topology. In my case  I have three different  "K" values, which "k" 
> value do I have to take, Can I take sum of all  the three "k" values 
> or can I take  arbitrary value.

Your table would need to be the weighted sum of the three cosines, so 
apparently you have not yet generated such a table. But rather than buy 
trouble, go and do the easier and faster solutions above :-)


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