[gmx-users] cutoff values for amber ff

[Jarmila Husby]

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.

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
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