From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Nov 02 2010 - 11:46:34 CDT
You need to use a newer version of NAMD (2.7b2 or later).
On Nov 2, 2010, at 11:33 AM, Christian Jorgensen wrote:
> Hi all,
> I am trying to perform the FEP tutorial simulation in step 1.2 (zero-sum transformation)
>
> However, upon running the simulation I get the following error:
>
> Info: Configuration file is junk.conf
> TCL: Running FEP window 1: Lambda1 0.0 Lambda2 0.0625 [dLambda 0.0625]
> TCL: Suspending until startup complete.
> ERROR: The following variables were set in the
> ERROR: configuration file but are NOT VALID
> ERROR: alchElecLamdaStart
> ERROR: alchVdwLamdaEnd
> ERROR: aclhCol
> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
> [0] Stack Traceback:
> [0:0] CmiAbort+0x93 [0xb3edfb]
> [0:1] _Z8NAMD_diePKc+0x62 [0x5241be]
> [0:2] _ZN13SimParameters22initialize_config_dataEP10ConfigListRPc+0x73 [0xa106c9]
> [0:3] _ZN9NamdState14configListInitEP10ConfigList+0x394 [0x97d222]
> [0:4] _ZN9ScriptTcl9initcheckEv+0x76 [0x9ee16c]
> [0:5] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x4a [0x9ea990]
> [0:6] TclInvokeStringCommand+0x91 [0xb73648]
> [0:7] TclExecuteByteCode+0x856 [0xb8df2f]
> [0:8] Tcl_EvalObjEx+0x2bb [0xb7405b]
> [0:9] TclObjInterpProc+0x2fa [0xbafe03]
> [0:10] TclExecuteByteCode+0x856 [0xb8df2f]
> [0:11] Tcl_EvalObjEx+0x2bb [0xb7405b]
> [0:12] TclObjInterpProc+0x2fa [0xbafe03]
> [0:13] /usr/local/NAMD_2.7b4_Linux-x86_64/namd2 [0xba9498]
> [0:14] Tcl_EvalEx+0x176 [0xba9adb]
> [0:15] Tcl_EvalFile+0x134 [0xba14e4]
> [0:16] _ZN9ScriptTcl3runEPc+0x2f [0x9ea17d]
> [0:17] _Z18after_backend_initiPPc+0x21f [0x5288bf]
> [0:18] main+0x3a [0x52866a]
> [0:19] __libc_start_main+0xf4 [0x3c3ac1d994]
> [0:20] _ZNSt8ios_base4InitD1Ev+0x52 [0x52378a]
> [0] Stack Traceback:
> [0:0] /usr/local/NAMD_2.7b4_Linux-x86_64/namd2 [0xb3fd85]
> [0:1] CmiAbort+0xd1 [0xb3ee39]
> [0:2] _Z8NAMD_diePKc+0x62 [0x5241be]
> [0:3] _ZN13SimParameters22initialize_config_dataEP10ConfigListRPc+0x73 [0xa106c9]
> [0:4] _ZN9NamdState14configListInitEP10ConfigList+0x394 [0x97d222]
> [0:5] _ZN9ScriptTcl9initcheckEv+0x76 [0x9ee16c]
> [0:6] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x4a [0x9ea990]
> [0:7] TclInvokeStringCommand+0x91 [0xb73648]
> [0:8] TclExecuteByteCode+0x856 [0xb8df2f]
> [0:9] Tcl_EvalObjEx+0x2bb [0xb7405b]
> [0:10] TclObjInterpProc+0x2fa [0xbafe03]
> [0:11] TclExecuteByteCode+0x856 [0xb8df2f]
> [0:12] Tcl_EvalObjEx+0x2bb [0xb7405b]
> [0:13] TclObjInterpProc+0x2fa [0xbafe03]
> [0:14] /usr/local/NAMD_2.7b4_Linux-x86_64/namd2 [0xba9498]
> [0:15] Tcl_EvalEx+0x176 [0xba9adb]
> [0:16] Tcl_EvalFile+0x134 [0xba14e4]
> [0:17] _ZN9ScriptTcl3runEPc+0x2f [0x9ea17d]
> [0:18] _Z18after_backend_initiPPc+0x21f [0x5288bf]
> [0:19] main+0x3a [0x52866a]
> [0:20] __libc_start_main+0xf4 [0x3c3ac1d994]
> [0:21] _ZNSt8ios_base4InitD1Ev+0x52 [0x52378a]
>
>
>
>
>
> I have defined my .conf file in the following way and I have done exactly as is being stated in the tutorial (including cleaning up my PSF file etc.)
>
>
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
>
> structure zero.psf
> coordinates setup.pdb
>
> set temperature 300
> set outputname fep_run1
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters common/par_all27_prot_lipid.inp
> temperature $temperature
>
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 10.
> pairlistdist 13.5
>
>
> # Integrator Parameters
> timestep 2.0 ;# 2fs/step
> rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
> #firsttimestep 0
>
>
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>
>
> # Periodic Boundary Conditions
> cellBasisVector1 21.8 0. 0.
> cellBasisVector2 0. 21.8 0.
> cellBasisVector3 0. 0 21.8
> cellOrigin 0. 0. 0.
>
> wrapAll on
>
>
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 22
> PMEGridSizeY 22
> PMEGridSizeZ 22
>
>
> # Constant Pressure Control (variable volume)
> useGroupPressure yes ;# needed for rigidBonds
> useFlexibleCell no
> useConstantArea no
>
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 100.
> langevinPistonDecay 50.
> langevinPistonTemp $temperature
>
>
> # Output
> outputName $outputname
>
> restartfreq 500 ;# 500steps = every 1ps
> dcdfreq 250
> xstFreq 250
> outputEnergies 100
> outputPressure 100
>
>
> #FEP parameters
>
> source fep.tcl
> alch on
> alchType FEP
> alchFile zero.fep
> aclhCol B
> alchOutFile forward-noshift.fepout
> alchOutFreq 10
>
> alchVdwLamdaEnd 1.0
> alchElecLamdaStart 1.0
> alchVdWShiftCoeff 0.0
> alchDecouple no
>
> alchEquilSteps 100
> set numSteps 500
>
> runFEP 0.0 1.0 0.0625 $numSteps
>
>
>
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Minimization
> minimize 100
> reinitvels $temperature
>
> run 2500 ;# 5ps
>
>
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>
> Any help would be much appreciated
>
> Christian
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