[gmx-users] questions about energy minimization

[Mark Abraham]

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