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: [email protected] tel: (44) 0207 753 5996
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