[gmx-users] cutoff values for amber ff

Justin A. Lemkul jalemkul at vt.edu
Thu Nov 18 20:06:26 CET 2010

Jarmila Husby wrote:
> Dear all,
> I am setting-up a simulation of a protein-DNA complex using amber  force 
> field.
> In the manual (v4.5.3) I have found the recommended cutoff distances for 
> electrostatics - coulombtype using PME (rcoulomb=rlist=rvdw = 0.9nm) 
> with Gromos ff. However, I am aware the cutoff values are specific for 
> different forcefield and also the simulated system.
> Since I am using the amber ff with Gromacs, I wanted to ensure I set-up 
> the correct cutoffs to prevent any potential artifacts, so I have 
> searched the manual, gmx-users old posts (gromacs wiki links do not work 
> any more) and papers, and I found all sorts of distances for the 
> non-bonded interactions tratment with PME (ranging from 1.0 to 1.4 nm).
> With respect to the amber ff, I found a value of 0.8nm cutoff for the 
> PME in the Amber manual.
> Could you please advise me on what would be the reasonable cutoff values 
> to choose for the protein-DNA system, with the use of Gromacs 4.5.3 and 
> amber ff?
> All your comments will be greatly appreciated.

You haven't searched in the most important location yet - the primary literature 
for your chosen force field (and there are subtle differences among the 
different Amber force fields).  It is generally recommended to follow the 
protocols used to derive the force field, in the absence of any subsequent 
modifications that demonstrate better results.


> Thank you
> Jarmila
> Jarmila Husby, PhD Candidate
> CRUK PPI Drug Discovery/ BMSG Group
> Department of Pharm & Biol Chemistry
> The School of Pharmacy, University of London
> email: jarmila.husby at live.pharmacy.ac.uk
> tel: (44) 0207 753 5996


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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