[gmx-users] charmm in gromacs cut-offs
tarak20489 at gmail.com
Fri May 17 11:37:33 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 read few posts in this issue
But the point, if I use rlist=rvdw then the dynamics will not be proper as
in the neighbor list updating and energy calculations. Now, the any kind of
change in the rlist essentially enforcing to change the coul cut-off. So,
rlist and coul-cut-off are not independent of each other.
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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