From: Jindal Shah (jindal.shah_at_gmail.com)
Date: Mon Mar 01 2010 - 09:11:47 CST
I am actually simulating crystobalite and adopting the FF of MacKerell as
was done in Nangia et al. JPhysChem B, 2007.
Irrespective, I cannot figure out why the dihedral energy blows up in the
very first step when all the dihedral K_chi terms
are set to zero.
On Sun, Feb 28, 2010 at 11:41 PM, Eduardo <chucruz_at_ks.uiuc.edu> wrote:
> 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
> 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
> 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?
> Eduardo Roberto Cruz Chu
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