[gmx-users] Using longer cut-off for AMBER99SB

Agnivo Gosai agnivogromacs14 at gmail.com
Fri Feb 26 20:22:33 CET 2016

Dear Users,

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
; Neighborsearching
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)
; Electrostatics
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
Agnivo Gosai
Grad Student, Iowa State University.

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