Re: Help, MD run errors

From: Xiaobing Tian (xiaobing_at_tesla.jci.tju.edu)
Date: Sun May 02 2004 - 21:06:58 CDT

Hi, everyone,
I am doing MD of my protein with PMF and periodic coundary conditions.
MD run resulted in a fatal error:
Periodic cell has become too small for original patch grid!(see attached
file).
Could anyone give me advice?(I used top_all27_prot_na.inp to prepare my
solvated .psf and .pdb files.)
I also attached my .config file(see attached file).

Thank you for your help.

Cheers,
Xiaobing

Info: Benchmark time: 1 CPUs 0.58171 s/step 3.36638 days/ns 34302 kB memory
ENERGY: 700 160.4422 424.8042 311.1816
28.8040 -34779.6804 3365.5629 0.0000
0.0000 5012.0515 -25476.8339 260.7847
-25462.0388 -25469.1159 252.2316 559.1239
594.6498 96444.8091 -43.1998 -42.5704

WRITING COORDINATES TO DCD FILE AT STEP 700
Info: Benchmark time: 1 CPUs 0.583407 s/step 3.3762 days/ns 34622 kB memory
FATAL ERROR: Periodic cell has become too small for original patch grid!
Possible solutions are to restart from a recent checkpoint,
increase margin, or disable useFlexibleCell for liquid simulation.
Stack Traceback:
 [0] _ZN9HomePatch13doMarginCheckEv+0x202 [0x81d702e]
 [1] _ZN9HomePatch14positionsReadyEi+0x7b [0x81d5ab7]
 [2] _ZN9Sequencer17runComputeObjectsEii+0xec [0x822c1b0]
 [3] _ZN9Sequencer9integrateEv+0x69f [0x822f2a7]
 [4] _ZN9Sequencer9algorithmEv+0x158 [0x822ba80]
 [5] _ZN9Sequencer9threadRunEPS_+0xc [0x82386b4]
 [6] namd2 [0x82758a4]
 [7] Charm++ Runtime: Converse thread (qt_args+0x66 [0x82c40aa])

Attached .config file:

>> #############################################################
>> ## JOB DESCRIPTION ##
>> #############################################################
>>
>> # Minimization and Equilibration of
>> # fvm in a Water Box
>>
>>
>> #############################################################
>> ## ADJUSTABLE PARAMETERS ##
>> #############################################################
>>
>> structure output/fvm_wb.psf
>> coordinates output/fvm_wb.pdb
>>
>> set temperature 310
>> set outputname output/fvm_wb
>>
>> firsttimestep 0
>>
>>
>> #############################################################
>> ## SIMULATION PARAMETERS ##
>> #############################################################
>>
>> # Input
>> paraTypeCharmm on
>> parameters par_all27_prot_na.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 49.52 0. 0.
>> cellBasisVector2 0. 45.89 0.
>> cellBasisVector3 0. 0 46.23
>> cellOrigin 7.61 4.75 3.94
>> wrapWater on
>> wrapAll on
>>
>>
>> # PME (for full-system periodic electrostatics)
>> PME yes
>> PMEGridSizeX 50
>> PMEGridSizeY 48
>> PMEGridSizeZ 48
>>
>>
>> # Constant Pressure Control (variable volume)
>> useGroupPressure yes ;# needed for rigidBonds
>> useFlexibleCell no
>> useConstantArea no
>>
>> langevinPiston on
>> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
>> langevinPistonPeriod 200.
>> langevinPistonDecay 100.
>> langevinPistonTemp $temperature
>>
>> # Output
>> outputName $outputname
>>
>> restartfreq 500 ;# 500steps = every 1ps
>> dcdfreq 100
>> xstFreq 100
>> outputEnergies 100
>> outputPressure 100
>>
>>
>> #############################################################
>> ## EXTRA PARAMETERS ##
>> #############################################################
>>
>>
>> #############################################################
>> ## EXECUTION SCRIPT ##
>> #############################################################
>>
>> # Minimization
>> minimize 500
>> reinitvels $temperature
>> output min_fix
>
>> run 10000 ;# 20ps
>
>

-- 
Xiaobing Tian, Ph.D.
Department of Biochemistry & Molecular Pharmacology
Thomas Jefferson University
233 South 10th Street, Suite 219
Philadelphia PA19107

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