Jia Haitao wrote:
Manual section 4.2.13 maybe not enough. My potential functional shape is
much more complex. I need at least two different force constants as C6
and C12 in LJ potential function in section 6.7.2.
I use this for block copolymer system. There is only two types of
monomer(e.g. A, B) and two types of bond potential(e.g.A-A, B-B ). If I
can form two tables related to the two different bond potential
respectively (e.g. table 1 for A-A and table 2 for B-B), the problem
will be solved. Is it possible to be done in Gromacs?
Yes. This is not terribly clear in the manual, so I will update it, but you can
indeed supply, i.e. table_b0.xvg, table_b1.xvg, table_b2.xvg, etc as necessary.
-Justin
On Tue, Dec 7, 2010 at 11:14 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Jia Haitao wrote:
Hello, everyone
In gromacs user manual 6.7, they form non-bond potentials using
table files, What should I do if I want to use a new *Bond*
potential? The new bond potential combines two harmonic bond
potentials, Vb(r)=0.5K1(r-b1)^2+0.5K2(r-b2)^2. The first part
is a standard harmonic potential.
Besides, according user manual 5.7, there is 10 function types
in table 5.5. How can I use the 8th and 9th type? Is there some
examples? .
All the information related to what you want to do is in the manual,
section 4.2.13. Per the caption of Table 5.5, bond type 8 will be
used to generate exclusions (when running grompp); presumably type 9
will not. Hopefully someone will correct me if I'm wrong here.
-Justin
--
*/
Jia Haitao
State Key Laboratory of Polymer Physics and Chemistry
Changchun Institute of Applied Chemistry
Chinese Academy of Sciences
Changchun 130022, CHINA
/*
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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*/
Jia Haitao
State Key Laboratory of Polymer Physics and Chemistry
Changchun Institute of Applied Chemistry
Chinese Academy of Sciences
Changchun 130022, CHINA
/*
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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