stereo-chemical inversion during MD

From: Gordon Wells (
Date: Mon May 07 2012 - 12:01:24 CDT

Hi All

I've encountered a strange situation when simulating a particular
conformation of L-Glu. During minimisation the bond angle between the
carboxyl-C, C-alpha and amino-N decreases from 112° to 89°. When this is
subsequently used for MD there is often a stereo-chemical inversion around
the C-alpha. I see this when simulating the system in its original protein
complex and free in solution (TIP3 solvent for both).

I can prevent it by using a very short minimisation (50 instead of 1000
steps), increasing the di-electric or decreasing the partial charges on the
ammonium hydrogens. Nonetheless, I'm sure this strained conformation
shouldn't be produced in the first place (I'm not able to replicate this
behaviour in macromodal or desmond) The force between the carboxyl oxygen
(nearest to the ammonium moiety) and the ammonium hydrogens seems to be too

I've attached before and after pdbs of the free L-glu. I get the distorted
conformation from the following namd input (with and without pbc):

coordinates LGlu_autopsf.pdb
structure LGlu_autopsf.psf

paratypecharmm on
parameters par_all27_prot_lipid_na.inp

outputname minall-lglu-only
binaryoutput yes
outputenergies 25

switching on
cutoff 12
switchdist 10
pairlistdist 14
exclude 1-4

fixedAtoms off

numsteps 1000
dielectric 1
minimization on

Is this forcefield related, bad input file or possibly a bug in NAMD?

-- max(∫(εὐδαιμονία)dt)

Dr Gordon Wells
Chemistry Department
Emory University
Atlanta, Georgia, USA

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