[gmx-users] questions about energy minimization

[DreamCatcher]

To whom may be concerned,
       I am just doing an energy minimization on a polymer chain ---PVA,
which contains 50 repeat units. I am puzzled about how to choose an
appropriate emtol. It's said to be a maximum force in the system. But how to
make sure that the emtol I choose is big or small enough that my system will
finally well equilibrium?  After I finished the energy minimization, when
the maximum force is actually under the emmtol, I compare the potential to a
previou energy minimization work using some other software like Material
Studio, It is the finally potential that surprise me a lot. The potential I
get using gromacs is still positive and with a magnitude of e~03 whist using
Material Studio it is negative and with the same magnitude.Why so? Is there
any reference I can refer to?
      Thanks in advanced.

celeste

2010-04-14
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