On 6/4/13 8:22 AM, vidhya sankar wrote:
Dear Justin Thank you for your Previuos reply
I am using gromos53a6 ff When i changed the parameters for cut-off (r list )
value to 1.2
I have got Error as follows What is the Meaning of Note 2 & 3
NOTE 2 [file cntcycpepfull2.mdp]:
The switch/shift interaction settings are just for compatibility; you
will get betterperformance from applying potential modifiers to your
interactions!
NOTE 3 [file cntcycpepfull2.mdp]:
For energy conservation with switch/shift potentials, rlist should be 0.1
to 0.3 nm larger than rcoulomb.
NOTE 4 [file cntcycpepfull2.mdp]:
For energy conservation with switch/shift potentials, rlist should be 0.1
to 0.3 nm larger than rvdw.
WARNING 1 [file cntcycpepfull2.mdp]:
The sum of the two largest charge group radii (0.518710) is larger than
rlist (1.200000) - rvdw (1.200000)
WARNING 2 [file cntcycpepfull2.mdp]:
The sum of the two largest charge group radii (0.518710) is larger than
rlist (1.200000) - rcoulomb (1.200000)
nstlist = 5
rlist = 1.2
rcoulomb = 1.2
vdwtype = Shift
rvdw = 1.2
coulombtype = Reaction-Field-zero
pme_order = 4
fourierspacing = 0.16
pcoupl = Parrinello-Rahman
pcoupltype = isotropic
thus .grompp terminated due to warnings
To Avoid his I have used the rlist=1.8 (in Above valuue) Because the difference
betwen rlist-rcoloum should Be greater than 0.518710
But you maild me the cut-off looks Bizarre .it should be based on parent force
field(mine is gromos53a6)
If you're using Gromos96 53A6, nearly all of your settings are wrong. Please
refer to the primary literature for the force field and the many posts in the
list archive regarding proper use of that force field. Making ad hoc changes
just to get grompp to stop complaining is a very error-prone way to do
simulations (which end up being unstable or invalid by doing so).
-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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