shahab shariati wrote:
Hi all
I am beginner in gromacs.
I want to simulate interaction between protein and dna. SPC model for
water, is suitable for amber03 force field.
The best idea is to do your homework. Read the paper for the original
derivation of AMBER03, and any subsequent work that has been done that may have
used the SPC water model. Generally, the AMBER force fields are used with
TIP3P, but that certainly does not preclude the possibility that another model
may be appropriate.
-Justin
--
========================================
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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