[gmx-users] Tabulated potentials for dihedrals - regd
rameshgromacs at gmail.com
Thu Jun 7 11:28:19 CEST 2012
I am very Thankful to you for your valuable suggestion.
On Thu, Jun 7, 2012 at 12:04 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> 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
> Thank you in advance.
> On Mon, Jun 4, 2012 at 12:55 PM, Mark Abraham <Mark.Abraham at 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 :-)
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