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. 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. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
