On 7/06/2012 4:33 AM, ramesh cheerla wrote:
Dear Mark,
Thank you for your reply, According to my
understanding functional form of dihedral function type 9 is same as
dihedral function type 1 i.e k (1 + cos(n (phi)- phi s)) except
the difference that function type 9 is used to handle the multiple
potential functions to be applied to the single dihedreal, Is my
understanding correct ?.
The functional form that I am using Summn over 'n' 0.5*K [ ( Cos
n(phi-phi0)] , Here 1<= n <= 3 is different from the k (1 + cos(n
(phi)- phi s)). I am suspecting can I use function type 9 for my
function.
Can you please clarify my doubt.
I said last time you can use type 9. You can use high-school maths to
express your equation in the form of a sum of multiple type 1, which is
type 9. The additive constant only affects the total energy, which is
never used for the simulation. The derivative of V is used, so the
constant goes away.
Mark
Thank you in advance.
On Mon, Jun 4, 2012 at 12:55 PM, Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>> wrote:
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 :-)
Mark
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