Well ... the answer is yes: pairs interactions are scaled by
if epsilon different than 1.0 is defined in the mdp file ...
but easier to fix that the shift/switch thingy ...
Another point (more scary) is that using fudge LJ = 0.0 does not turn
off the pairs LJ interactions; fudge QQ does for electrostatic!
this is using the standard gmx-4.0.7 ...
---------------------------------------
some numbers for the purists:
----------------------------------------
epsilon = 2.5; fudge LJ = 1.0; fudge QQ = 0.5
Step Time Lambda
0 0.00000 0.00000
Energies (kJ/mol)
Bond Tab. Angles Improper Dih. Tab. Dih.
LJ-14
1.56855e+02 3.84067e+01 1.68183e+01 -1.36500e+03
2.26253e+01
Coulomb-14 LJ (SR) Coulomb (SR) Potential
Kinetic En.
7.92958e+01 -1.41790e+05 -2.97492e+02 -1.43139e+05
2.07062e+04
Total Energy Temperature Pressure (bar)
-1.22432e+05 3.07112e+02 -2.18939e+01
----------------------------------------
epsilon = 25; fudge LJ = 1.0; fudge QQ = 0.5
Energies (kJ/mol)
Bond Tab. Angles Improper Dih. Tab. Dih.
LJ-14
1.56855e+02 3.84067e+01 1.68183e+01 -1.36500e+03
2.26253e+01
Coulomb-14 LJ (SR) Coulomb (SR) Potential
Kinetic En.
7.92958e+00 -1.41790e+05 -2.97493e+01 -1.42942e+05
2.07033e+04
Total Energy Temperature Pressure (bar)
-1.22239e+05 3.07069e+02 -2.01929e+01
----------------------------------------
epsilon = 25; fudge LJ = 0.0; fudge QQ = 0.5
Energies (kJ/mol)
Bond Tab. Angles Improper Dih. Tab. Dih.
LJ-14
1.56855e+02 3.84067e+01 1.68183e+01 -1.36500e+03
2.26253e+01
Coulomb-14 LJ (SR) Coulomb (SR) Potential
Kinetic En.
7.92958e+00 -1.41790e+05 -2.97493e+01 -1.42942e+05
2.07033e+04
Total Energy Temperature Pressure (bar)
-1.22239e+05 3.07069e+02 -2.01929e+01
----------------------------------------
epsilon = 25; fudge LJ = 0.0; fudge QQ = 0.0
Energies (kJ/mol)
Bond Tab. Angles Improper Dih. Tab. Dih.
LJ-14
1.56855e+02 3.84067e+01 1.68183e+01 -1.36500e+03
2.26253e+01
Coulomb-14 LJ (SR) Coulomb (SR) Potential
Kinetic En.
0.00000e+00 -1.41790e+05 -2.97493e+01 -1.42950e+05
2.07033e+04
Total Energy Temperature Pressure (bar)
-1.22247e+05 3.07069e+02 -2.02610e+01
On Feb 10, 2010, at 5:59 PM, XAvier Periole wrote:
Dears,
One questions about pair interaction. I mean the one defined in the
topology files under the [ pairs ].
They interaction with plain electrostatic, meaning without shift,
switch
function applied to it. If it was possible to change this, it would be
pretty nice, unless there are specific use for this ...
The question: Does the pairs electrostatic interactions include an
eventual
epsilon ?
Thanks,
XAvier.
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