[gmx-users] Positive potential energies for Dimethyl Aniline and Aniline
debayan.ch at gmail.com
Sun May 6 17:42:25 CEST 2012
I am trying to build a well equilibrated solvent
box of aniline and N,N dimethyl aniline using the OPLS-AA parameters. I
have built my topolgy files by closely following that given for
2-chloroaniline in the molecule and liquids database of virualchemistry.org.
I have even downloaded the files of chloroaniline and ran short
simulations. In those simulations I get negative potential and total
energies, and even the Coulomb-recip term is negative.
When I switch to my systems aniline and DMA, for both I get negative
potential energies for the minimized structure. However, the coulomb-recip
term is positive in both cases. When I start my MD total energies for both
aniline and DMA become positive, though aniline still retains a negative
value of potential energy, the potential for DMA becomes positive.
My questions are : Are positive or negative energies of a system during
simulation real indicators of something wrong in your MD ?
How is it possible that chloroaniline, aniline
and DMA which are closely related systems have so different values of
Does a positive Coulomb recip term indicate
wrong representation of electrostatics ?
For all the systems I have used the charges from the OPLS-AA force field.
Any help in this matter will be greatly appreciated. I have tried to think
hard about these issues but my limited knowledge about simulations have not
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