On 1/16/18 10:24 AM, kordza...@aut.ac.ir wrote:
Hi every one
I have a question
I want to obtain topology of carbon nano tube with x2top but I must determine
the value of bond strength and angle constant.
I think we have a bond carbon-carbon that stretches with a constant force for
example in amber force field this constant is 392459 kj /(mol nm^2) for
interaction CA-CA but in gromos force field this constant is define
differently....
There is no meaningful comparison that can be made between any
parameters in different force fields. They all use different
parametrization conventions, and in this case you're looking at AMBER
(all-atom) vs. GROMOS (united-atom) and therefore aspects of the atoms
themselves will be different (e.g. heavier masses on aliphatic C in GROMOS).
I don't know what should I do
I 'm confused, in gromos
define gb_17 0.14 8.5400E+6
C,CR1,CH2
8.54 e 6 is force constant for stretch bond and dimention is kj/(mol nm^2), am
I right?
No; GROMOS uses a quartic bond potential. See the manual and the
discussion on this topic from yesterday.
then we can conclude that if I want to determine force constant , I must select
these constant wwith respect to force field ,
I can't say these constants are same every where.rigth?
is the dimention of constant kj/(mol nm^2) every where in gromacs, such as .itp
files of force field, itp files that we receive form ATB and so on?
any suggestion will be appreciated
If you need to develop new parameters or validate ones you have, you
need to follow the methodology prescribed by the force field you're
trying to use. For bonded force constants, this typically requires a QM
vibrational frequency calculation and empirical fitting to reproduce the
vibrational modes.
-Justin
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==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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