Re: ERROR: Multiple definitions of 'LangevinPiston'

From: roberta.rostagno (roberta.rostagno_at_unimib.it)
Date: Wed May 20 2009 - 09:44:02 CDT

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@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@ks.uiuc.edu>
>> To: "roberta.rostagno" <roberta.rostagno@unimib.it>
>> Cc: <namd-l@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@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@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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