From: Christian Jorgensen (christian.jorgensen_at_merton.ox.ac.uk)
Date: Tue Nov 02 2010 - 11:33:12 CDT
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
Any help would be much appreciated
Christian
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