On 6/4/13 11:25 AM, vidhya sankar wrote:
Dear Justin Thank you for yoyr Previuos reply
I am using
Gromos96 53a6
so i am using the following parameters
ns_type = grid
nstlist = 5
rlist = 0.9
rcoulomb = 0.9
rvdw = 1.4
is this value is reasonable ?
Yes.
But when i run the grommp i got warnings as follows
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
NOTE 2 [file CNTPEPnvt.mdp]:
You are using a cut-off for VdW interactions with NVE, for good energy
conservation use vdwtype = Shift (possibly with DispCorr)
NOTE 3 [file CNTPEPnvt.mdp]:
You are using a cut-off for electrostatics with NVE, for good energy
conservation use coulombtype = PME-Switch or Reaction-Field-zero
if Chnge vdwtupe=shift with disspCorr = DispCorr = EnerPres
I have got the error as follows
WARNING 2 [file CNTPEPnvt.mdp]:
The sum of the two largest charge group radii (0.498722) is larger than
rlist (0.900000) - rvdw (1.400000)
How to to Avoid this error? (Due to warning grompp_d terminated )
The notes and warnings arise from settings that are still incorrect. Gromos96
force fields do not use shifted potentials for vdW interactions; they are simply
truncated at rvdw using a plain cutoff. The plain cutoff for Coulombic
interactions is also wrong. The original Gromos96 development was done with a
reaction field term, but more recent work has shown PME to be superior.
-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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