Does MOLLY really retain bond motion for water?

From: Francesco Pietra (
Date: Sun Jun 02 2013 - 08:45:04 CDT


I have a problem with a water molecule bound to Zn(II) in a metal cluster
of a protein, under parm7 amber ff. As I posted before (unanswered), by
setting "rigidBonds water", NAMD 2.9-CUDA hangs, asking for bond parameters
for the two H-atoms of the water molecule bound to Zn(II). Although the
whole cluster, such water included, is called MOL.

By not freezing any bond, the simulation goes on smoothly, albeit slowly.
Therefore, I have now tried to retain all bond motions by the use of MOLLY,
of which I had no previous experience, with multiple timesteps. Got the
same error message, asking for params as said above. In all cases,
"timestep 1.00" The relevant portion of the conf file:

## colvars
colvars on # provide a colvarsConfig (and colvarsINput if restart)
colvarsConfig ./
colvarsInput ./press-01.restart.colvars.state

## Output
restartfreq 1000
dcdfreq 1000
xstFreq 1000
outputEnergies 6000
outputPressure 1000
outputname ./press_molly-02

## AMBER FF settings
amber on
# rigidBonds water
#useSettle on
# rigidTolerance 1.0e-8
molly on
mollytolerance 0.00001
mollyiterations 100
cutoff 9.0
pairlistdist 11.0
switching off
exclude scaled1-4
readexclusions yes
1-4scaling 0.83333333
scnb 2.0
zeromomentum on
ljcorrection on
watermodel tip3

## Integrator Parameters
timestep 1.00
nonbondedFreq 2 # ts between nonbonded eval
fullElectFrequency 6 # number ts between full electrostatic eval
stepspercycle 12
margin 0

Which error related to MOLLY in conf file? If none, I wonder whether MOLLY
really retains bond motions for water, or the way MOLLY does that is
different by allwing all bond motions by the traditional flags.


francesco pietra

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