On 6/4/13 9:48 PM, vidhya sankar wrote:
Dear Justin Thank you for your Previous reply.
As yo mailed me The Defaut Value for vandewalls and Electrostatics in
GROMOS96 53A6 is PME option
s_type = grid
nstlist = 5
rlist = 0.9
rcoulomb = 0.9
rvdw = 1.4
But in you Umbrella sampling you are using GROMOS96 53A6 FF there
you quoted different Parameters in your em.mdp file
nstlist = 1 ; Frequency to update the neighbor list and long range
forces
ns_type = grid ; Method to determine neighbor list (simple, grid)
rlist = 1.4 ; Cut-off for making neighbor list (short range forces)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.4 ; Short-range electrostatic cut-off
rvdw = 1.4 ; Short-range Van der Waals cut-off
pbc = xyz
can i Take 1.4 instead of 0.9 value
The value of rcoulomb is a bit more flexible when using PME, but unless you have
a basis for changing it (and having demonstrated that the change is harmless),
you shouldn't deviate from the parameters given for the force field.
oterwise is there is Any spcification according to system and BOx size
The contents of the system and size of the box do not dictate the parameters
that are set; the force field does.
-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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