From: Eduardo (chucruz_at_ks.uiuc.edu)
Date: Sun Feb 28 2010 - 22:41:09 CST
The high energy can be due to constraints in your structure, but it
can also be due to a mistake in your PSF assignment.
As far as I remember, they provided all silica structures in the
supplementary materials of their paper. Just need to use those ones.
On Feb 28, 2010, at 9:51 PM, Jindal Shah wrote:
> Hello NAMD users,
>
> I am trying to minimize a silica block generated from crystobalite
> crystal structure.
> The force field I am using is that from Lopez and MacKerell. The
> starting
> structure is in highly strained conformation for this FF and the
> minimization
> fails in the first step step as it cannot generate search
> direction. The initial energies
> for dihedral angles is 999999999.99. Even if setting all the
> dihedral constants K_chi
> to zero, I have not been able to get this energy to go to zero. It
> is calculated to be
> the same as before.
>
> Any suggestions?
> Thanks,
> Jindal
=====================
Eduardo Roberto Cruz Chu
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