From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed May 20 2009 - 09:59:45 CDT
Roberta,
are these exactly the config files that you used? If you look at the
logfile from your first run, does it actually print output from 20000
steps of minimization? You have the minimize 20000 line enclosed in a
block that won't be evaluated...
At the end of the minimization in your second run, what gradient values
are being listed? You should also look at the immediate environment of
the atoms that are giving the RATTLE errors. You can, for example, get
rattle errors if you include harmonic restraints (constraints in
NAMD-ese) on hydrogen atoms and the associated heavy atoms that are not
compatible with their rigid bond length.
Best,
Peter
roberta.rostagno wrote:
> Dear Peter,
> I activated PME in minimization and minimized the system with fixed
> atoms for 20000 steps and this is the config file:
> amber yes
> parmfile M52SKIresp.prmtop
> ambercoor M52SKIresp.prmcrd
> readexclusions off
> outputname 1M52SKIrespsimulatedannealing
> restartName 1m52SKIrespsimannrest
>
> set temperature 0
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> temperature $temperature
>
>
> # Periodic Boundary conditions
> # NOTE: Do not set the periodic cell basis if you have also
> # specified an .xsc restart file!
> cellBasisVector1 88. 0. 0.
> cellBasisVector2 0. 88 0.
> cellBasisVector3 0. 0 88.
> cellOrigin -0.00 -0.16 0.26
>
> wrapAll on
>
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 0.833333
> cutoff 12.
> switching on
> switchdist 10.
> pairlistdist 14.0
>
>
>
>
> # Integrator Parameters
> timestep 1;# 1 fs/step
> numsteps 20000
> rigidBonds all ;# needed for 2fs steps
> rigidTolerance 0.0005
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
>
> #PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 90
> PMEGridSizeY 90
> PMEGridSizeZ 90
>
>
>
> restartfreq 200 ;# 500steps = every 1ps
> dcdfreq 100
> outputEnergies 100
> outputPressure 100
>
> dcdfile 1m52SKIrespsimann.dcd
>
> # Fixed Atoms Constraint (set PDB beta-column to 1)
> if {0} {
> fixedAtoms on
> fixedAtomsFile fix.pdb
> fixedAtomsCol B
> }
>
> minimization on
> if {0} {
> minimize 20000
> reinitvels $temperature
> }
> -------------------------------
> and it runs ok until the end
>
> then I used the restart files to run another config file for simulated
> annealing (config file:)
>
>
> amber yes
> parmfile M52SKIresp.prmtop
> ambercoor M52SKIresp.prmcrd
> readexclusions off
> outputname 1M52SKIrespMDsimulatedannealing
> restartName 1m52SKIrespMDsimannrest
>
> # Continuing a job from the restart files
> binCoordinates 1m52SKIrespsimannrest.coor
> binVelocities 1m52SKIrespsimannrest.vel ;# remove the
> "temperature" entry if you use this!
> extendedSystem 1m52SKIrespsimannrest.xsc
> #
> firsttimestep 20000
> #
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> wrapAll on
>
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 0.833333
> cutoff 12.
> switching on
> switchdist 10.
> pairlistdist 14.0
>
>
>
>
> # Integrator Parameters
> timestep 1;# 1 fs/step
> numsteps 11822000
> rigidBonds all ;# needed for 2fs steps
> rigidTolerance 0.0005
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
>
> #PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 90
> PMEGridSizeY 90
> PMEGridSizeZ 90
>
>
> restartfreq 200 ;# 500steps = every 1ps
> dcdfreq 1
> outputEnergies 100
> outputPressure 100
>
> dcdfile 1m52SKIrespMDsimann.dcd
> constraints on
> consRef restrain.pdb
> consKFile restrain.pdb
> consKCol B
> #constraintScaling 50
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
> reassignFreq 1000
> reassignTemp 0
> minimize 1000
> for { set TEMP 0 } {$TEMP<601} {incr TEMP 1} {
> run 1000
> reassignTemp $TEMP
> }
> run 500000
> for { set TEMP 600 } {$TEMP>=300} {incr TEMP -1} {
> reassignTemp $TEMP
> run 1000
> }
> run 500000
> run 4000000
>
> reassignFreq 1000
> reassignTemp 0
> minimize 1000
> for { set TEMP 0 } {$TEMP<601} {incr TEMP 1} {
> run 1000
> reassignTemp $TEMP
> }
> run 500000
> for { set TEMP 600 } {$TEMP>=300} {incr TEMP -1} {
> reassignTemp $TEMP
> run 1000
> }
> run 500000
> run 4000000
> -------------------------------------------------
> after few minimization step I have the warning message:
>
> Warning: Bad global exclusion count, possible error!
> Warning: Increasing cutoff during minimization may avoid this.
>
> but the 1000 steps of minimization go.
> then the calculation crash:
> TCL: Running for 1000 steps
> REASSIGNING VELOCITIES AT STEP 21000 TO 0 KELVIN.
> ERROR: Constraint failure in RATTLE algorithm for atom 2178!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Constraint failure in RATTLE algorithm for atom 2658!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Constraint failure in RATTLE algorithm for atom 2301!
> etc.....
>
>
> I saved the dcd file every steps but it seems ok. Nothing wrong appens
> near the end of minimization.
> Can you help me to solve this problem?
> thank you in advance
>
>
> Roberta Rostagno
>
>
>
>
>
> On Fri, 15 May 2009 05:54:11 -0500
> Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> > Hi Roberta,
> > you certainly can use the restart coor, vel, and xsc
> >files, but you must
> > still include the PME block in each restart -- you have
> >it deactivated
> > by an if {0} in the config file that you posted. The
> >restart files
> > contain **only** information on the coordinates,
> >velocities, and system
> > size, not on whether pme is being used or any other
> >simulation
> > parameters. If you use the exact same config file but
> >include the PME
> > settings, things should be fine.
> > Peter
> >
> > Roberta Rostagno wrote:
> >> Dear Peter,
> >> I want run calculation with PME, soi I have to use
> >>Periodic boundary
> >> condition. What I have to do? Can I use restart coor and
> >>velocity files
> >> and not xsc? And I have to measure again dimension and
> >>center of the box
> >> in order to indicate them in the periodic boundary
> >>conditions input?
> >> Thank you for your answer.
> >> roberta
> >> ----- Original Message ----- From: "Peter Freddolino"
> >> <petefred_at_ks.uiuc.edu>
> >> To: "roberta.rostagno" <roberta.rostagno_at_unimib.it>
> >> Cc: <namd-l_at_ks.uiuc.edu>
> >> Sent: Thursday, May 14, 2009 5:19 PM
> >> Subject: Re: namd-l: ERROR: Multiple definitions of
> >>'LangevinPiston'
> >>
> >>
> >>> Hi Roberta,
> >>> do you really mean to be running without PME?
> >>>
> >>> In general, the errors that you're seeing generally
> >>>indicate that the
> >>> system is becoming unstable. This could be because PME
> >>>has been turned
> >>> off, or because minimization got stuck, or some other
> >>>reason. I'd
> >>> recommend starting your simulated annealing run while
> >>>writing the dcd
> >>> every timestep, so that you can see what the system is
> >>>doing immediately
> >>> before it crashes.
> >>> Best,
> >>> Peter
> >>>
> >>> roberta.rostagno wrote:
> >>>> Dear all,
> >>>> I decided to run minimization and simulated annealing
> >>>>with different
> >>>> conf files. I've just finished the minimization step
> >>>> (100000 steps with
> >>>> minimization on command). When I run the simulated
> >>>>annealing the
> >>>> calculation doesn't start because of the error:
> >>>>
> >>>> ERROR: Constraint failure in RATTLE algorithm for atom
> >>>>1952!
> >>>> ERROR: Constraint failure; simulation has become
> >>>>unstable.
> >>>>
> >>>> repeated for 30 atoms. I had a look at the structure
> >>>>obtained from the
> >>>> minimization but all the atoms seem ok.
> >>>>
> >>>> If I run also a little minimization (1000 steps with
> >>>>minimize command)
> >>>> before the simulated annealing, the calculation starts
> >>>>and gives be back
> >>>> the warning:
> >>>>
> >>>> bad exclusion count.
> >>>> after minimization 1000 steps, when sim ann should
> >>>>start, I obtain the
> >>>> same error as before and the calculation aborts.
> >>>>
> >>>> Anyone have some suggestion to solve the problem?
> >>>>
> >>>>
> >>>> conf file:
> >>>>
> >>>>
> >>>> amber yes
> >>>> parmfile M52SKIresp.prmtop
> >>>> ambercoor M52SKIresp.prmcrd
> >>>> readexclusions off
> >>>> outputname 1M52SKIrespMDsimulatedannealing
> >>>> restartName 1m52SKIrespMDsimannrest
> >>>>
> >>>> set temperature 0
> >>>> # Continuing a job from the restart files
> >>>> if {1} {
> >>>> set inputname M52SKIMDsimann
> >>>> binCoordinates 1m52SKIrespsimannrest.coor
> >>>> binVelocities 1m52SKIrespsimannrest.vel ;# remove
> >>>>the
> >>>> "temperature" entry
> >>>> if you use this!
> >>>> extendedSystem 1m52SKIrespsimannrest.xsc
> >>>> }
> >>>>
> >>>> firsttimestep 20000
> >>>> # NOTE: Do not set the initial velocity temperature if
> >>>>you
> >>>> # have also specified a .vel restart file!
> >>>> #temperature $temperature
> >>>> # Periodic Boundary conditions
> >>>> # NOTE: Do not set the periodic cell basis if you have
> >>>>also
> >>>> # specified an .xsc restart file!
> >>>> #if {0} {
> >>>> #cellBasisVector1 88. 0. 0.
> >>>> #cellBasisVector2 0. 88 0.
> >>>> #cellBasisVector3 0. 0 88.
> >>>> #cellOrigin -0.00 -0.16 0.26
> >>>> #}
> >>>> wrapAll on
> >>>> # Force-Field Parameters
> >>>> exclude scaled1-4
> >>>> 1-4scaling 0.833333
> >>>> cutoff 12.
> >>>> switching on
> >>>> switchdist 10.
> >>>> pairlistdist 14.0
> >>>> # Integrator Parameters
> >>>> timestep 1;# 1 fs/step
> >>>> #numsteps 11802000
> >>>> rigidBonds all ;# needed for 2fs steps
> >>>> rigidTolerance 0.0005
> >>>> nonbondedFreq 1
> >>>> fullElectFrequency 2
> >>>> stepspercycle 10
> >>>> #PME (for full-system periodic electrostatics)
> >>>> if {0} {
> >>>> PME yes
> >>>> PMEGridSizeX 90
> >>>> PMEGridSizeY 90
> >>>> PMEGridSizeZ 90
> >>>> }
> >>>> # Constant Temperature Control
> >>>> langevin on ;# do langevin dynamics
> >>>> langevinDamping 5 ;# damping coefficient (gamma)
> >>>>of 5/ps
> >>>> langevinTemp $temperature
> >>>> langevinHydrogen no ;# don't couple langevin bath
> >>>>to hydrogens
> >>>> # Constant Pressure Control (variable volume)
> >>>> if {0} {
> >>>> useGroupPressure yes ;# needed for 2fs steps
> >>>> useFlexibleCell no ;# no for water box, yes for
> >>>>membrane
> >>>> useConstantArea no ;# no for water box, yes for
> >>>>membrane
> >>>>
> >>>> langevinPiston on
> >>>> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> >>>> langevinPistonPeriod 200.
> >>>> langevinPistonDecay 100
> >>>> langevinPistonTemp $temperature
> >>>> }
> >>>> restartfreq 200 ;# 500steps = every 1ps
> >>>> dcdfreq 100
> >>>> outputEnergies 100
> >>>> outputPressure 100
> >>>> dcdfile 1m52SKIrespMDsimann.dcd
> >>>>
> >>>> constraints on
> >>>> consRef restrain.pdb
> >>>> consKFile restrain.pdb
> >>>> consKCol B
> >>>> #############################################################
> >>>> ## EXECUTION SCRIPT
> >>>> ##
> >>>> #############################################################
> >>>> reassignFreq 1000
> >>>> #reassignTemp 0
> >>>> minimize 1000
> >>>> for { set TEMP 0 } {$TEMP<601} {incr TEMP 1} {
> >>>> reassignTemp $TEMP
> >>>> run 1000
> >>>> }
> >>>> run 500000
> >>>> for { set TEMP 600 } {$TEMP>=300} {incr TEMP -1} {
> >>>> reassignTemp $TEMP
> >>>> run 1000
> >>>> }
> >>>> run 500000
> >>>> run 4000000
> >>>>
> >>>> reassignFreq 1000
> >>>> #reassignTemp 0
> >>>> minimize 1000
> >>>> for { set TEMP 0 } {$TEMP<601} {incr TEMP 1} {
> >>>> reassignTemp $TEMP
> >>>> run 1000
> >>>> }
> >>>> run 500000
> >>>> for { set TEMP 600 } {$TEMP>=300} {incr TEMP -1} {
> >>>> reassignTemp $TEMP
> >>>> run 1000
> >>>> }
> >>>> run 500000
> >>>> run 4000000
> >>>>
> >>>> regards
> >>>>
> >>>> Roberta Rostagno
> >>>>
> >>>>
> >>>> On Tue, 12 May 2009 06:41:29 -0500
> >>>> Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> >>>>> Hi Roberta,
> >>>>> could you include a little more context, say, up through
> >>>>> the first "run"
> >>>>> statement that you think should be doing dynamics? From
> >>>>> what I see here,
> >>>>> it looks like in the first case you're not doing any
> >>>>> minimization at all
> >>>>> due to the if statement, which would certainly explain a
> >>>>> bad global
> >>>>> exclusion count (or several other errors that boil down
> >>>>> to starting
> >>>>> dynamics from a badly strained conformation).
> >>>>> Peter
> >>>>>
> >>>>> roberta.rostagno wrote:
> >>>>>> Hi Peter,
> >>>>>>
> >>>>>> This is the config file with minimize:
> >>>>>> #############################################################
> >>>>>> ## EXECUTION SCRIPT
> >>>>>> ##
> >>>>>> #############################################################
> >>>>>>
> >>>>>> #Minimization
> >>>>>> if {0} {
> >>>>>> minimize 10000
> >>>>>> reinitvels $temperature
> >>>>>> }
> >>>>>> and this is the config file with minimization on
> >>>>>> command:
> >>>>>>
> >>>>>> minimization on
> >>>>>> if {0} {
> >>>>>> minimize 20000
> >>>>>> reinitvels $temperature
> >>>>>> }
> >>>>>> I would like to run MD with periodic boundary conditions
> >>>>>> and PME. If I
> >>>>>> use restart files the boundary conditions are read by
> >>>>>> the .xsc file? SO
> >>>>>> I can omit periodic boundary conditions information but
> >>>>>> I have to
> >>>>>> specify PME information in the config file?
> >>>>>>
> >>>>>> thanks
> >>>>>>
> >>>>>> Roberta
> >>>>>>
> >>>>>> On Mon, 11 May 2009 12:11:57 -0500
> >>>>>> Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> >>>>>>> Hi Roberta,
> >>>>>>>
> >>>>>>> roberta.rostagno wrote:
> >>>>>>>> Thank you for your answer. If I don't use minimization
> >>>>>>>> on, but only
> >>>>>>>> minimize command after few steps I have the error:
> >>>>>>>> bad global exclusion clount. Instead with minimization
> >>>>>>>> on the
> >>>>>>>> minimization run without errors until the end.
> >>>>>>>
> >>>>>>> I can't think of any reason for minimize n and
> >>>>>>> minimization on; run n to
> >>>>>>> yield different results... could you send me snippets of
> >>>>>>> the end of the
> >>>>>>> relevant config files?
> >>>>>>>
> >>>>>>> Bad global exclusion count errors generally indicate an
> >>>>>>> overly long bond
> >>>>>>> in the system... can you visually inspect your structure
> >>>>>>> and make sure
> >>>>>>> it looks ok?
> >>>>>>>
> >>>>>>> By the way, is namd terminating upon the exclusion count
> >>>>>>> error? During
> >>>>>>> minimization, bad global exclusion counts should give a
> >>>>>>> warning but not
> >>>>>>> an error.
> >>>>>>>
> >>>>>>>> if I run minimization and MD with different conf file,
> >>>>>>>> can I use restart
> >>>>>>>> coordinate and velocity files obtained from minimization
> >>>>>>>> to start MD?
> >>>>>>>> thanks again for help
> >>>>>>>
> >>>>>>> Yes; you can read the coordinates, velocities, and
> >>>>>>> extended system from
> >>>>>>> the previous run with bincoordinates, binvelocities, and
> >>>>>>> extendedSystem,
> >>>>>>> respectively (they'll be named
> >>>>>>> $outputname.restart.coor/vel/xsc)
> >>>>>>>
> >>>>>>> By the way, are you sure you mean to be running without
> >>>>>>> pme?
> >>>>>>> Also, that rigid bond tolerance is quite large...
> >>>>>>>
> >>>>>>> Best,
> >>>>>>> Peter
> >>>>>>>
> >>>>>>
> >>>>>
> >>>>
> >
>
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