Re: [AMBER] Minimization Question

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Mon, 11 Jul 2011 19:15:35 -0700

> I have a convergence problem in minimization step.
> My system is a di-molecular system. The molecules have extra-points.
> Minimization of each molecule separate finished properly. But
> minimization of the two molecules complex couldn't reach minimization.
> I found the energy is the exactly the same after 200 minimization
> cycles, but RMS changes. Comparing to the starting structure (QM level),
> the MM structure is exactly the same.
> What tricks could be used to reach minimization?

Minimization usually gives a structure that is visually pretty much
superimposable on the original, unless you have some strain in the system,
such as long bonds or vdw overlaps. To explore more configuration space
and find lower energy, low-temperature molecular dynamics is worth a
try, in vacuum. I would suggest 10K and 100K for an initial look.


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Received on Mon Jul 11 2011 - 19:30:04 PDT
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