On 5/18/13 7:58 AM, tarak karmakar wrote:
Dear All,
It seems the problem in the cut-off schemes while using charmm force
field in gromacs persists even in the latest gromacs-4.6.1 version.
Recently I have posted regarding this problem came in gromacs-4.5.5
version. If anybody has already tested this issue in the latest version,
please leave a comment in the mailing list.
The cut-off parameters I have used are as follows
rlist = 1.2
rlistlong = 1.4
; 7.3.10 Electrostatics
coulombtype = PME
rcoulomb = 1.2
; 7.3.11 VdW
vdwtype = switch
rvdw = 1.2
rvdw-switch = 1.0
NOTE 3 [file md_sim_ann.mdp]:
The switch/shift interaction settings are just for compatibility; you
will get better performance from applying potential modifiers to your
interactions!
NOTE 4 [file md_sim_ann.mdp]:
For energy conservation with switch/shift potentials, rlist should be 0.1
to 0.3 nm larger than rvdw.
NOTE 5 [file md_sim_ann.mdp]:
The sum of the two largest charge group radii (0.079732) is larger than
rlist (1.200000) - rvdw (1.200000)
This part is reported as bug in gromacs -4.5.5 and required to be verified
by users through their feedback
http://redmine.gromacs.org/issues/1164
In this link it is showing affected version grom-4.6.1 !!
There are a lot of conditionals that are evaluated and probably (as Mark has
indicated) some of them are conflicting. What you have posted above seems
correct from my interpretation of everything I have read about using CHARMM.
Since all you are getting are notes (rather than errors), you shouldn't have any
problems.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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