From: Marcos Sotomayor (sotomayo_at_ks.uiuc.edu)
Date: Fri Apr 21 2006 - 09:17:00 CDT
Hi Martin,
Likely the problem is caused because you are trying to increase the
temperature gradually while you have Langevin Temperature control on.
Turn off Langevin, heat the system gradually, and then turn on Langevin in
your next run to keep the temperature of your system steady.
Marcos
On Fri, 21 Apr 2006, Martin Loewer wrote:
> Hello,
>
> when starting a dynamics simulation, minimization runs well and it always
> (tried serveral times) runs until setp 1000 and produces the following error
> message (end of log file):
>
> WRITING COORDINATES TO DCD FILE AT STEP 1000
> WRITING COORDINATES TO RESTART FILE AT STEP 1000
> FINISHED WRITING RESTART COORDINATES
> WRITING VELOCITIES TO RESTART FILE AT STEP 1000
> FINISHED WRITING RESTART VELOCITIES
> TCL: Setting parameter reassignFreq to 100
> FATAL ERROR: Setting parameter reassignFreq from script failed!
>
> Stack Traceback:
> [0] CmiAbort+0x51 [0x734751]
> [1] _Z8NAMD_diePKc+0x63 [0x49ab63]
> [2] _ZN13SimParameters9scriptSetEPKcS1_+0x4be [0x66dea6]
> [3] _ZN4Node11scriptParamEP14ScriptParamMsg+0x25 [0x617a25]
> [4] _ZN12CkIndex_Node32_call_scriptParam_ScriptParamMsgEPvP4Node+0x12
> [0x6179fa]
> [5] CkDeliverMessageFree+0x30 [0x6cfe38]
> [6] _Z15_processHandlerPvP11CkCoreState+0x44a [0x6d24ca]
> [7] CmiHandleMessage+0x26 [0x73b1ae]
> [8] CsdScheduleForever+0x4b [0x73b30b]
> [9] CsdScheduler+0x1c [0x73c98c]
> [10] _ZN7BackEnd7suspendEv+0xe [0x4a1536]
> [11] _ZN7BackEnd7barrierEv+0xe [0x4a14fe]
> [12] _ZN9ScriptTcl12setParameterEPKcS1_+0x137 [0x657a27]
> [13] _ZN9ScriptTcl9Tcl_paramEPvP10Tcl_InterpiPPc+0x18c [0x65697c]
> [14] TclInvokeStringCommand+0x91 [0x758d78]
> [15] /home/loewer/bin/NAMD/namd2 [0x78ebc8]
> [16] /home/loewer/bin/NAMD/namd2 [0x78e9e1]
> [17] Tcl_EvalEx+0x176 [0x78f20b]
> [18] Tcl_EvalFile+0x134 [0x786c14]
> [19] _ZN9ScriptTcl3runEPc+0x1c [0x656294]
> [20] main+0x222 [0x49dae2]
> [21] __libc_start_main+0xda [0x2aaaab12a5aa]
> [22] _ZStlsISt11char_traitsIcEERSt13basic_ostreamIcT_ES5_c+0x5a [0x49a4aa]
>
> This looks like a bug in the program to me. Maybe I can change my config file
> (see below) to avoid this.
>
> Sincerly,
> Martin Loewer
>
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
> structure sp_wb.psf
> coordinates sp_wb.pdb
> set temperature 310
> set outputname sp_wb_eq
> firsttimestep 0
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
> # Input
> paraTypeCharmm on
> parameters 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
>
> # 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 82. 0. 0.
> cellBasisVector2 0. 90. 0.
> cellBasisVector3 0. 0 90.
> cellOrigin 29.0915279388 -18.3676776886 17.4208488464
> wrapAll on
>
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 96
> PMEGridSizeY 96
> PMEGridSizeZ 96
>
> # 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
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
> # Minimization
> minimize 1000
>
> ## Heating Process
> reassignFreq 100
> reassignTemp 31
> reassignIncr 31
> reassignHold $temperature
> reinitvels 31
> run 3500 ;# 7ps
>
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