Re: ERROR: Multiple definitions of 'LangevinPiston'
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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: Wed Feb 29 2012 - 15:52:48 CST