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,
JCTC'
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
"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
http://lists.gromacs.org/pipermail/gmx-users/2013-February/079037.html
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.
Thanks,
Tarak
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
