[gmx-users] pairs interactions

[XAvier Periole]

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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