Dear gromacs users, I am using gromacs 4.5.3, OPLSAA force field, and the cut off parameters are as shown below: --------------------------------------------------------------------------------------------- ;NEIGHBOURSEARCHING PARAMETERS nstlist = 10 10 ; FREQUENCY WITH WHICH NEIGHBOURLIST IS UPDATED ns_type = grid ; TYPE OF NEIGHBOUR SEARCH GRID OR SIMPLE pbc = xyz ; DIRECTION OF PERIODIC BOUNDARY CONDITIONS USAGE rlist = 1.36 ; CUT-OFF DISTANCE FOR SHORT RANGE NEIGHBOUR LIST
;ELECTROSTATICS coulombtype = PME ; METHOD FOR CALCULATING COULOMBIC INTERCATION - PME rcoulomb = 1.36 ; CUTOFF DISTANCE FOR ELECTROSTATIC INTERACTIONS epsilon_r = 1 ; RELATIVE DIELECTRIC CONSTANT ;VAN DER WAALS vdwtype = Switch ; METHOD FOR TREATING VANDERWAAL'S FORCES rvdw_switch = 0.9 ; WHEN TO START SWITCHING LJ POTENTIAL rvdw = 1.03 ; CUTOFF DISTANCE FOR LJ OR BUCKINGHAM INTERACTIONS ;EWALD fourierspacing = 0.12 ; GRID SPACING FOR FFT GRID FOR PME pme_order = 4 ; INTERPOLATION ORDER FOR PME ewald_rtol = 1e-5 ; RELATIVE STRENGTH OF EWALD SHIFTED DIRECT POTENTIAL optimize_fft = yes ; SAVES A FEW PERCENT FOR LONG SIMULATIONS ----------------------------------------------------------------------------------------------------- For EM (energy minimisation) I initially had used rlist = rcolomb = 1.2; rvdw = 1.1; rvdw_switch = 1.0 grompp gave the message: ################## Largest charge group radii for Van der Waals: 0.160, 0.157 nm Largest charge group radii for Coulomb: 0.168, 0.167 nm NOTE 1 [file md.mdp]: The sum of the two largest charge group radii (0.317) is larger than rlist (1.20000) - rvdw (1.10000) ################## So I changed the values to: rlist = rcolomb = 1.35; rvdw = 1.03; rvdw_switch = 1.0 grompp message during em disappeared. During PR (position refinement), Again the message appeared for grompp ################## Largest charge group radii for Van der Waals: 0.168, 0.156 nm Largest charge group radii for Coulomb: 0.168, 0.164 nm NOTE 1 [file md.mdp]: The sum of the two largest charge group radii (0.324) is larger than rlist (1.35000) - rvdw (1.03000) ################## hence I changed the values to: rlist = rcolomb = 1.36; rvdw = 1.03; rvdw_switch = 1.0 grompp message during pr disappeared. The same message repeated for MD ################### Largest charge group radii for Van der Waals: 0.171, 0.159 nm Largest charge group radii for Coulomb: 0.171, 0.166 nm NOTE 1 [file md.mdp]: The sum of the two largest charge group radii (0.330248) is larger than rlist (1.360000) - rvdw (1.030000) ################### My questions are: 1. Why does the charge group radii change in this way from em to pr to MD even though I am using same parameters 2. What is the safest maximum value of rlist I can go up to? (is it 1.4nm according to "The Origin of Layer Structure Artifacts in Simulations of Liquid Water"- JCTC, 2006, 2, 1-11 paper?) 3. What is the minimum safest rvdw distance i can take? 4. According to the manual, when using switch they have suggested that ".. neighbor search cut-off rlist should be 0.1 to 0.3nm larger than rvdw..." then Why in the above case it goes more than 0.3nm? Thanks in advance MKS
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