[gmx-users] About Physical parameters

[vidhya sankar]

Dear Justin Thank you for your Previuos reply

                                                                                I am using gromos53a6 ff When i changed the parameters for cut-off  (r list ) value to 1.2 

I have got Error as follows  What is the Meaning of Note 2 & 3


NOTE 2 [file cntcycpepfull2.mdp]:
  The switch/shift interaction settings are just for compatibility; you
  will get betterperformance from applying potential modifiers to your
  interactions!

NOTE 3 [file cntcycpepfull2.mdp]:
  For energy conservation with switch/shift potentials, rlist should be 0.1
  to 0.3 nm larger than rcoulomb.
NOTE 4 [file cntcycpepfull2.mdp]:
  For energy conservation with switch/shift potentials, rlist should be 0.1
  to 0.3 nm larger than rvdw.

WARNING 1 [file cntcycpepfull2.mdp]:
  The sum of the two largest charge group radii (0.518710) is larger than
  rlist (1.200000) - rvdw (1.200000)

WARNING 2 [file cntcycpepfull2.mdp]:
  The sum of the two largest charge group radii (0.518710) is larger than
  rlist (1.200000) - rcoulomb (1.200000)

nstlist        = 5 

rlist        = 1.2
rcoulomb    = 1.2 

vdwtype         = Shift
rvdw        = 1.2
coulombtype    =  Reaction-Field-zero 

pme_order    = 4
fourierspacing    = 0.16
pcoupl        = Parrinello-Rahman 

pcoupltype    = isotropic   

thus .grompp terminated due to warnings

To Avoid his I have used the rlist=1.8 (in Above valuue) Because the difference betwen rlist-rcoloum should Be greater than 0.518710 

But you maild me the cut-off looks Bizarre .it should be based on parent force field(mine is gromos53a6)

I hope  your  kind Suugestion are useful to get succesfull production mdrun
Thanks In ADVANCE