abelius wrote:
Since the charges / bond lengths and angles were obtained for QM
calculations for the excited state of TRP I'm wondering if it would make
sense to apply the alternative bond lengths and keep the force constants
of TRP in the ground state?
I guess it's really going to depend on whether or not any of the bonded
interactions are altered by this excited state. If, for example, your excited
state changes the bond order of a particular bond (i.e., promotion of an
electron in a bonded orbital to one in an antibonding orbital), then I would
argue that the force constants in the force field are incorrect, since that bond
would thus be weakened.
-Justin
Cheers,
Abel
Justin A. Lemkul wrote:
abelius wrote:
But How can I determine this constant? (I guess using the one of
normal TRP would make no sense)
I would suggest reading the primary literature for your force field of
interest. How did the original authors assign these parameters?
Usually bonded information comes from experimental data (spectroscopy,
etc.)
-Justin
Thanks,
Abel
Justin A. Lemkul wrote:
abelius wrote:
Thank you for your reply,
I was just struggling to get the ffxxxbon.rtp syntax right since I
only have atom distances to create the bonds.
So can anyone tell me what the correct syntax is for these defines
in the ffxxxbon.rtp file?
#define <name> <distance in nm?> <?>
? = force constant
Furthermore where and how can I add the angle information?
Angles are defined similarly
#define <name> <equilibrium angle> <force constant>
-Justin
Thanks,
Abel
Gerrit Groenhof wrote:
You can use #define's
Like
[ bonds ]
C1 C2 e_c1c2
Then in the ffxxxbon.rtp
you define these things explicitly
#define e_c1c2 0.15 123445
Gerrit
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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