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
>>>>>>>
>>>>>>
>>>>>
>>>>
>