[gmx-users] Re: gmx-users digest, Vol 1 #653 - 10 msgs

[Yuguang Mu]

Dear all,
I have implanted AMBER force field into the GROMACS-3.1.4.
I have check the vacuum energy of peptide, nucleic acids compared with
original AMBER data, the energies difference between gromacs and original
amber  are less than 0.1%.

Here when I want to simulate molecules in water, using PME, I found that
all the system including waters, solutes have translational motions
building up. The system is moving faster and faster.

I am little worry about my implantation of amber in gromacs that gromacs
uses charge group concept, while in AMBER there is no such charge group,
so I just randomly choose charge groups in the molecule.

This fast overall translation of whole system has no relation with initial
states. Because I have remove the overall translation in the equilibrium
stages.

Do you think such fast overall translation of whole system has some thing
with PME or charge groups ?


Dr. Yuguang Mu
Institute for Physical and Theoretical Chemistry
J.W. Goethe University Frankfurt am Main
Marie Curie Str. 11
60439 Frankfurt/Main, Germany
Tel: +49-(0)69-798-29711