Re: ERROR: Multiple definitions of 'LangevinPiston'

From: roberta.rostagno (roberta.rostagno_at_unimib.it)
Date: Thu May 14 2009 - 04:02:29 CDT

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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