[gmx-users] Ligand simulation

[Kavyashree M]

Dear users,

Although this topic has been extensively discussed
in the list previously, I am unclear about the solution
for the problem..

While running ligand in water simulation (EM) with RF-0
I get the following message:

----------------------------------------------------------------------------------------------------------
Number of degrees of freedom in T-Coupling group rest is 24531.00
Largest charge group radii for Van der Waals: 0.458, 0.356 nm
Largest charge group radii for Coulomb:       0.458, 0.356 nm

NOTE 1 [file ../em.mdp]:
  The sum of the two largest charge group radii (0.814337) is larger than
  rlist (1.600000) - rvdw (1.000000)

NOTE 2 [file ../em.mdp]:
  The sum of the two largest charge group radii (0.814337) is larger than
  rlist (1.600000) - rcoulomb (1.400000)
----------------------------------------------------------------------------------------------------------

But I continued for nvt and npt where I got the
same notes
NVT -
----------------------------------------------------------------------------------------------------------
Largest charge group radii for Van der Waals: 0.509, 0.487 nm
Largest charge group radii for Coulomb:       0.509, 0.487 nm

NOTE 1 [file ../nvt.mdp]:
  The sum of the two largest charge group radii (0.996343) ....

NOTE 2 [file ../nvt.mdp]:
  The sum of the two largest charge group radii (0.996343) .....

----------------------------------------------------------------------------------------------------------
for NPT -

Number of degrees of freedom in T-Coupling group System is 16357.00
Largest charge group radii for Van der Waals: 0.787, 0.684 nm
Largest charge group radii for Coulomb:       0.787, 0.684 nm

NOTE 1 [file ../npt.mdp]:
  The sum of the two largest charge group radii (1.470764) .....

NOTE 2 [file ../npt.mdp]:
  The sum of the two largest charge group radii (1.470764) .....
----------------------------------------------------------------------------------------------------------

For MD -
----------------------------------------------------------------------------------------------------------
Largest charge group radii for Van der Waals: 0.671, 0.605 nm
Largest charge group radii for Coulomb:       0.671, 0.605 nm

NOTE 1 [file md.mdp]:
  The sum of the two largest charge group radii (1.276104) ......

NOTE 2 [file md.mdp]:
  The sum of the two largest charge group radii (1.276104) .....
----------------------------------------------------------------------------------------------------------


The ligand is not broken, whole of it is inside the water in the
beginning of the simulation, topology is ok because protein-ligand
simulation with PME ran fine.

Any suggestions are welcome.

Thank you
Regards
kavya