[gmx-users] Implementation of CHARMM setup in GROMACS

francesco oteri francesco.oteri at gmail.com
Tue Feb 26 17:30:26 CET 2013

Dear gromacs users,
in Bjelkmar et al. (2010) where the implementation of CHARMM in GROMACS is
the authors say that:

"Electrostatics was treated with particle-mesh Ewald (PME), using a
short-range cutoff of
1.2 nm, and van der Waals interactions were switched off between 1.0 to 1.2

I translated this protocol in the following line in mdp file:

; Neighborsearching
rlist           = 1.2           ; short-range neighborlist cutoff (in nm)

; Electrostatics
coulombtype     = PME           ; Particle Mesh Ewald for long-range
rcoulomb           = 1.2           ; short-range electrostatic cutoff (in
vdwtype            = Switch
rvdw                 = 1.2           ; short-range van der Waals cutoff (in
rvdw_switch       = 1.0

But grompp complains:
NOTE 1 [file 02md.mdp]:
  For energy conservation with switch/shift potentials, rlist should be 0.1
  to 0.3 nm larger than rvdw.

If I enlarge rlist to 1.3, grompp genrates an error:
ERROR 1 [file 02md.mdp]:
  With coulombtype = PME, rcoulomb must be equal to rlist
  If you want optimal energy conservation or exact integration use

So, how can the protocol described in the paper has been implemented?

Should I use:
coulombtype     = PME-Switch


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