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

[Justin Lemkul]

On 2/26/16 2:22 PM, Agnivo Gosai wrote:
> 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)
> method."
>
> 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
> electrostatics
> 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.
>

Cutoffs are part of the force field.  If I had a nickel for every time I said 
that...

Replace the phrase "not required" with "not ever recommended without strong 
demonstration and justification that you're not breaking anything" and you'd be 
right.

> So, if I need to satisfy reviewer comments then do I need to show
> equivalent simulation data as in the original ff paper.
>

You should repeat at least a subset of your simulations with the correct cutoffs 
and (hopefully) demonstrate that the ensemble average properties do not differ 
significantly.  Depending on how many different types of systems you simulated, 
this may be a fair amount of work, reinforcing the importance of getting it 
right the first time :)

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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