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On 7/06/2012 4:33 AM, ramesh cheerla wrote:
<blockquote
cite="mid:CAPNFZqdMgq51DSML9jqGaFYdWvJoLdnxaPKcFjucahMxqiZnWA@mail.gmail.com"
type="cite">Dear Mark,<br>
<br>
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 ?.<br>
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.<br>
Can you please clarify my doubt.<br>
</blockquote>
<br>
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.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAPNFZqdMgq51DSML9jqGaFYdWvJoLdnxaPKcFjucahMxqiZnWA@mail.gmail.com"
type="cite"><br>
Thank you in advance.<br>
<div class="gmail_quote">On Mon, Jun 4, 2012 at 12:55 PM, Mark
Abraham <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt
0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class="im">On 4/06/2012 3:46 AM, ramesh cheerla wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex">
Dear Gromacs experts,<br>
<br>
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).<br>
</blockquote>
<br>
</div>
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.
<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt
0.8ex;border-left:1px solid
rgb(204,204,204);padding-left:1ex"> 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.<br>
</blockquote>
<br>
</div>
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 :-)<span class="HOEnZb"><font
color="#888888"><br>
<br>
Mark<br>
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