Re: Faltal Error. reassignFreq fails

From: Marc Q. Ma (qma_at_oak.njit.edu)
Date: Mon Apr 24 2006 - 10:53:46 CDT

Martin,

Your problem occurs at the 1000th step,which is right after
minimization. and i doubt 1000 steps min are enough for any
system ... you might need to increase this number.

Also, maybe you should try to separate the two protocols (min +
heating) into two separate runs, one for min, one for heating. And
turn on the parameters as needed in each run.

I wonder why you use 12 as cutoff while using PME. usually using a
large cutoff is advisable for simple N^2 naive pairwise
electrostatics. you should make it smaller, such as 6-9, to increase
the efficiency of the summation of the real term of the pme forces.

good luck!

marc
On Apr 24, 2006, at 10:18 AM, Martin Loewer wrote:

> 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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