[gmx-users] Tabulated potentials for dihedrals - regd

[Mark Abraham]

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.Abraham at anu.edu.au 
> <mailto: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 :-)
>
>     Mark
>     -- 
>     gmx-users mailing list gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20120607/a38b8e03/attachment.html>