[gmx-users] Using longer cut-off for AMBER99SB
agnivogromacs14 at gmail.com
Fri Feb 26 20:22:33 CET 2016
I have checked in the forum about posts using longer cut-off against those
used in the original force-field paper.
I am using AMBER99SB ff (Hornak et al. 2006) and the ff paper says "A
cutoff of 8-Å was used for nonbonded interactions, and long-range
electrostatic interactions were treated with the particle mesh Ewald (PME)
In my simulations, I have used
ns_type = grid ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist = 1.4 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)
rvdw = 1.4 ; short-range van der Waals cutoff (in nm)
coulombtype = PME ; Particle Mesh Ewald for long-range
pme_order = 4 ; cubic interpolation
fourierspacing = 0.12 ; grid spacing for FFT
So the cut-offs for non bonded interactions are much larger in my case. I
used a longer cut-off thinking that it would be more accurate. But, in some
of the earlier gromacs forum post I find that it is not required.
So, if I need to satisfy reviewer comments then do I need to show
equivalent simulation data as in the original ff paper.
Thanks & Regards
Grad Student, Iowa State University.
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