From: Wendy González (locuswendy_at_gmail.com)
Date: Fri Jan 07 2011 - 15:18:20 CST
Dear Athanassios:
The fact is that I use the same script (see below) in the 3 systems (they
change only in the charge of one histidine residue), and only one of them
have problems, the other run normally.
This is my script:
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure ionized.psf
coordinates DM_5ns_only_70.coor
velocities DM_5ns_only_70.vel
extendedSystem DM_5ns_only_70.xsc
parameters par_all27_lipid.prm
parameters par_all22_prot_cmap.inp
paraTypeCharmm on
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 13.5
# Integrator Parameters
timestep 0.5 ;# 1fs/step (2)
rigidBonds all ;# needed for 1fs steps (2)
nonbondedFreq 2
fullElectFrequency 4
stepspercycle 20
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1.0 ;# damping coefficient (gamma) of 10/ps (5)
langevinTemp 300
langevinHydrogen no ;# don't couple langevin bath to hydrogens
# use lighter damping now that system is equilibrated
langevinPiston on
langevinPistonTarget 1.01325
langevinPistonPeriod 200
langevinPistonDecay 500
langevinPistonTemp 310
useGroupPressure yes # smaller fluctuations
useFlexibleCell yes # allow dimensions to fluctuate
independently
useConstantRatio yes # fix shape in x-y plane
margin 2
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 103
PMEGridSizeY 103
PMEGridSizeZ 88
# Output
binaryoutput no
outputEnergies 10000
outputTiming 10000
xstFreq 10000
dcdFreq 10000
restartfreq 10000
############################################
if {1} {
constraints on
consRef restrain_ca_not_filter.pdb
consKFile restrain_ca_not_filter.pdb
consKCol B
}
##############################################################
outputname DM_5ns_E70x6times
run 10000
reloadCharges charges_only_task3_E70x6times.txt
run 5000000
2011/1/7 Athanassios Stavrakoudis <astavrak_at_cc.uoi.gr>
>
> Dear Wendy,
>
> Multiple reasons may lead to this situation.
> Most possibly, your system is not well minimized/equilibrated.
> You need to give a more detailed description of your simulation
> setup, to get more detailed answer.
> Also search the NAMD-l archives, almost any user has come with this
> problem.
>
> You can try to decrease the timestep to 1 fs,
> or to decrease the nonbondedFreq, fullElectFrequency values.
> Or to experiment with a mixture of all of these.
>
> Good luck,
> Thanassis
> > Dear NAMD Users,
> >
> > I am working with 3 systems, the only difference between them are:
> >
> > a) 2 histidines protonated
> > b) 1 histidine protonated, the second is neutral
> > c) Both histidines neutral
> >
> > I run several nanoseconds of simulations on this systems and they did not
> > have problems. I applied the reloadCharges command (increasing the charge
> of
> > the same glutamate in the 3 systems) and the results are:
> >
> > a) Run normally
> > b) ERROR: Constraint failure in RATTLE algorithm for atom XXXX ERROR:
> > Constraint failure; simulation has become unstable.
> > c) Run normally
> >
> > In case b) I said "atom XXXX", because I run 3 different simulations and
> the
> > error is with a different atom each time.
> >
> > Any suggestion??? What could be happening???
> >
>
>
>
> Athanassios Stavrakoudis
> University of Ioannina web:
> http://stavrakoudis.econ.uoi.gr/
> Department of Economics e-mail: mailto:astavrak_at_cc.uoi.gr
> GR-45110, Ioannina tel: +30 265 100 5935
> GREECE fax: +30 265 100 5092
>
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