On 14/04/2010 1:28 PM, DreamCatcher wrote:
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?
That depends on the purpose to which you intend to put it. For
preparation for MD, so long as the subsequent equilibration process
doesn't explode, you minimized enough.
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?
That will mean you have something nonphysical in your structure file
(e.g. overlapping atoms) or model physics (broken parameters or file
formats). In such cases EM may or may not help.
Mark
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