On 2/25/13 10:05 PM, Yun Shi wrote:
Hi all,
If I want do MD simulation with amber ff and implicit solvent, would
including gbsa.itp in .top file and specifying parameters in .mdp as
follows be sufficient?
implicit_solvent = GBSA
gb_algorithm = OBC
nstgbradii = 1.0
rgbradii = 1.0
In my experience, only infinite cutoffs (rvdw=rcoulomb=rlist=rgbradii=0) lead to
stable simulations. In my hands, even commonly applied "long cutoffs" (2.0 -
4.0 nm) lead to structural deformations.
gb_epsilon_solvent = 78.3
gb_dielectric_offset = 0.009
sa_algorithm = Ace-approximation
sa_surface_tension = 0.0054
But I wonder if this line is problematic in gbsa.itp: ";Br
0.1 1 1 0.125 0.85 ; H". Is this for a bromine
atom or hydrogen?
It's commented out, so it's irrelevant. The line should probably be removed,
though.
-Justin
[ implicit_genborn_params ]
; atype sar st pi gbr hct
;Br 0.1 1 1 0.125 0.85 ; H
C 0.172 1 1.554 0.1875 0.72 ; C
CA 0.18 1 1.037 0.1875 0.72 ; C
....
Regards,
Yun
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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