[gmx-users] charmm in gromacs cut-offs

tarak karmakar tarak20489 at gmail.com
Fri May 17 11:06:19 CEST 2013

Dear All,

I'm using charmm force field for simulation of a protein ligand system.
I have read the paper "implementation of charmm in gromacs by Bjelkmar,
They have used the following set up

coulombtype             = PME
rcoulomb                = 1.2

vdwtype                 = switch
rvdw                    = 1.2
rvdw-switch             = 1.0

Now, with this same set up if I use

rlist = 1.2
rlistlong =1.4

It is showing the following warning

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

Now, if I try to increase the rlist as rlist =1.3
Coulomb part is showing warning as

*ERROR 1 [file 02md.mdp]:**    With coulombtype = PME, rcoulomb must
be equal to rlist**   If you want optimal energy conservation or exact
integration use** PME-Switch*

I came across this post in the mailing list

But the point, if I use rlist=rvdw then the dynamics will not be proper as
in the neighbor list updating and energy calculations.

Can any one suggest me the best possible use of these parameters?
I am using gromacs-4.5.5 for simulations.


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