Re: ERROR: Multiple definitions of 'LangevinPiston'

From: Roberta Rostagno (roberta.rostagno_at_unimib.it)
Date: Fri May 15 2009 - 02:19:09 CDT

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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