From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon May 11 2009 - 08:09:40 CDT
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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