[gmx-users] charge group radii larger that rlist-rvdw

[Kavyashree M]

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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