From: Martin Loewer (m.loewer_at_cns.uni-frankfurt.de)
Date: Mon Apr 24 2006 - 09:18:02 CDT
Hi,
I followed your advice, but still I get the same error message at the
same timestep (1000).
My new config script is added below.
Are there any other reasons for the error?
Martin Loewer
structure sp_wb.psf
coordinates sp_wb.pdb
set temperature 310
set outputname sp_wb_heat
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters par_all27_prot_lipid.inp
temperature $temperature
# Output
binaryrestart yes
# 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 off ;# no langevin dynamics
# 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 off
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
# Minimization
minimize 1000
## Heating Process
reassignFreq 100
reassignTemp 31
reassignIncr 31
reassignHold $temperature
reinitvels 31
run 1500 ;# 3 ps
Marcos Sotomayor schrieb:
>
> 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
>>
>>
>
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