Re: ERROR: Multiple definitions of 'LangevinPiston'

From: roberta.rostagno (roberta.rostagno_at_unimib.it)
Date: Mon May 11 2009 - 08:20:29 CDT

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.
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

Roberta Rostagno

On Mon, 11 May 2009 08:09:40 -0500
  Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
> Hi Roberta,
> if I didn't know any better, I'd say that your problem
>is because you
> defined langevinPiston more than once in your config
>file, and namd
> doesn't like that.
> By the way, you don't need to use
> minimization on
> to get the conjugate gradient minimizer; just put in a
> minimize xxxx
> line to minimize for xxxx steps. You should be able to
>do this in a run
> with langevinPiston on (the pressure control just won't
>be active during
> minimization.
> You could also just do minimization in one run and
>dynamics in
> subsequent runs... there's no law that states that one
>has to do one's
> simulations in as few config files as possible.
> Best,
> Peter
>
> roberta.rostagno wrote:
>> Dear all,
>> I'm e new namd user. I would like to perform a
>>minimization and MD on e
>> protein+ligand+water system with AMBER imput files
>> My conf file is:
>>
>>
>> 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!
>> 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 0.5;# 1 fs/step
>> numsteps 23624000
>> 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 1m52SKIrespsimann.dcd
>> # Fixed Atoms Constraint (set PDB beta-column to 1)
>> if {0} {
>> fixedAtoms on
>> fixedAtomsFile fix.pdb
>> fixedAtomsCol B
>> }
>> constraints on
>> consRef restrain.pdb
>> consKFile restrain.pdb
>> consKCol B
>> #############################################################
>> ## EXECUTION SCRIPT ##
>> #############################################################
>> langevinpiston off
>> Minimization on
>> if {0} {
>> minimize 20000
>> reinitvels $temperature
>> }
>> fixedatoms off
>> langevinpiston on
>> reassignFreq 2000
>> reassignTemp 0
>> minimize 2000
>> for { set TEMP 0 } {$TEMP<601} {incr TEMP 1} {
>> reassignTemp $TEMP
>> run 2000
>> }
>> run 1000000
>> for { set TEMP 600 } {$TEMP>=300} {incr TEMP -1} {
>> reassignTemp $TEMP
>> run 2000
>> }
>> run 1000000
>> run 8000000
>> reassignFreq 2000
>> reassignTemp 0
>> minimize 2000
>> for { set TEMP 0 } {$TEMP<601} {incr TEMP 1} {
>> reassignTemp $TEMP
>> run 2000
>> }
>> run 1000000
>> for { set TEMP 600 } {$TEMP>=300} {incr TEMP -1} {
>> reassignTemp $TEMP
>> run 2000
>> }
>> run 1000000
>> run 8000000
>>
>> Minimization command doesn't work with langevin piston
>>on, so I have to
>> switch it off for minimization and then switch to on to
>>run MD.
>>
>> When namd analyze the conf file the bottom error is
>>written out and the
>> program stops.
>> Someone could help me to solve the problem?
>>
>> ERROR: Multiple definitions of 'LangevinPiston'
>> ERROR: in the configuration file are not allowed
>> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
>>
>>
>> Thank in advance
>>
>> Roberta

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