ROHIT MALSHE wrote:
Hi all,
I want to simulate a molecule which has many benzene rings attached to each
other. However I want to coarsegrain the system a lot !!
I want to represent the center of masses of benzene rings with point masses.
For all the parameters, such as bonds, angles, dihedrals I can use similar
parameters as these are very rigid molecules but I am confused what Lennard
Jones parameters should I use for these super atoms !
Can someone suggest how I can iteratively do that starting from a first guess
?
The best advice for developing parameters (for any type of system) is to read
relevant literature, decide on a derivation scheme, and set to work. There is
no substitute for doing your own homework!
-Justin
Any suggestions are most welcome !
__________________________________________________________________________________________________________
Rohit Malshe 1112,
Engineering Hall Tel :001 608 262 3370
Graduate Student 1415,
Engineering Drive Email: mal...@wisc.edu Chemical and Biological
Engineering Madison, WI. University of Wisconsin-Madison USA
USA- 53726
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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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