[gmx-users] charmm in gromacs cut-offs
tarak20489 at gmail.com
Fri May 17 11:11:07 CEST 2013
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
It is showing the following warning
"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
"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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