From: Suranga Edirisinghe (nerangedi_at_gmail.com)
Date: Mon Aug 27 2012 - 12:28:30 CDT
Hi
127011 ATOMS
Is this atom numbers includes water. if so I would check this values
PERIODIC CELL BASIS 1 1015.77 0 0
PERIODIC CELL BASIS 2 0 1432.08 0
PERIODIC CELL BASIS 3 0 0 1354.43
As you have water bubble (as you mentioned in other post) in your
simulation, this values may be wrong.
Thanks
Suranga
On Sun, Aug 26, 2012 at 12:07 PM, Mariana Graterol <
marianagraterol_at_gmail.com> wrote:
> Hi namd's support team:
>
> I work with NAMD 2.7b1 for Win32 in a personal computer with
>
> 6 AMD FX(tm)-6100 Six-Core Processor and 8 Gb of ram memory.
>
>
> I were doing an equilbration run of my protein system, with pbc, in NPT
> ensamble; then, when I reached constante pressure, total energy, temp. etc,
> and when I want to switch to an NVT ensamble, I can't begin the calculation
> with restart option because it appears a fatal error with the number of
> processors (at the end of this post I describe briefly).
>
>
> I checked the output files of my NPT run, I guess not having a constant
> volume cell size changes, as expected, but it increases from aprox. 120 x
> 120 x120 until 1100 x 1100 x 1100 AA, which is huge to PME calculation, as
> reflected in the size of the grid that is needed for.
>
>
> How can I fix this bug? or how can I restart the calculation with my new
> conditions - constant pressure, no cell volume constant-?
>
>
> Thank you to anyone who read this message...
>
> Mariana
>
>
> ***************************************************************
>
>
>
> Info: Based on Charm++/Converse 60100 for multicore-win32
>
> Info: Built Mon Mar 23 10:43:08 CDT 2009 by jcphill on honor
>
> Info: Running on 6 processors.
>
> Info: Charm++/Converse parallel runtime startup completed at 0 s
>
> Info: 0 MB of memory in use based on nothing
>
>
> ***TCL: Suspending until startup complete.
>
> Info: SIMULATION PARAMETERS:
>
> Info: TIMESTEP 1
>
> Info: NUMBER OF STEPS 400000
>
> Info: STEPS PER CYCLE 20
>
> Info: PERIODIC CELL BASIS 1 1015.77 0 0
>
> Info: PERIODIC CELL BASIS 2 0 1432.08 0
>
> Info: PERIODIC CELL BASIS 3 0 0 1354.43
>
> Info: PERIODIC CELL CENTER 1.5e-005 -3.8e-005 -4.6e-005
>
> Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
>
> Info: LOAD BALANCE STRATEGY New Load Balancers -- ASB
>
> Info: LDB PERIOD 4000 steps
>
> Info: FIRST LDB TIMESTEP 100
>
> Info: LAST LDB TIMESTEP -1
>
> Info: LDB BACKGROUND SCALING 1
>
> Info: HOM BACKGROUND SCALING 1
>
> Info: PME BACKGROUND SCALING 1
>
> Info: MAX SELF PARTITIONS 20
>
> Info: MAX PAIR PARTITIONS 8
>
> Info: SELF PARTITION ATOMS 154
>
> Info: SELF2 PARTITION ATOMS 154
>
> Info: PAIR PARTITION ATOMS 318
>
> Info: PAIR2 PARTITION ATOMS 637
>
> Info: MIN ATOMS PER PATCH 100
>
>
>
> ***
>
> Info: SWITCHING ON 8
>
> Info: SWITCHING OFF 12
>
> Info: PAIRLIST DISTANCE 12
>
> Info: PAIRLIST SHRINK RATE 0.01
>
> Info: PAIRLIST GROW RATE 0.01
>
> Info: PAIRLIST TRIGGER 0.3
>
> Info: PAIRLISTS PER CYCLE 2
>
> Info: PAIRLISTS ENABLED
>
> Info: MARGIN 0
>
> Info: HYDROGEN GROUP CUTOFF 2.5
>
> Info: PATCH DIMENSION 14.5
>
> Info: ENERGY OUTPUT STEPS 1000
>
> Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
>
> Info: TIMING OUTPUT STEPS 10000
>
> Info: HARMONIC CONSTRAINTS ACTIVE
>
> Info: HARMONIC CONS EXP 2
>
> Info: INTERACTIVE MD ACTIVE
>
> Info: INTERACTIVE MD PORT 3000
>
> Info: INTERACTIVE MD FREQ 20
>
> Info: LANGEVIN DYNAMICS ACTIVE
>
> Info: LANGEVIN TEMPERATURE 300
>
> Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS
>
> Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
>
> Info: PARTICLE MESH EWALD (PME) ACTIVE
>
> Info: PME TOLERANCE 1e-006
>
> Info: PME EWALD COEFFICIENT 0.257952
>
> Info: PME INTERPOLATION ORDER 4
>
> Info: PME GRID DIMENSIONS 1024 1440 1440
>
> Info: PME MAXIMUM GRID SPACING 1
>
> Info: Attempting to read FFTW data from FFTW_NAMD_2.7b1_Win32.txt
>
> Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
>
> Info: Writing FFTW data to FFTW_NAMD_2.7b1_Win32.txt
>
> Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 4
>
> Info: USING VERLET I (r-RESPA) MTS SCHEME.
>
> Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
>
> Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
>
> Info: RANDOM NUMBER SEED 12345
>
> Info: USE HYDROGEN BONDS? NO
>
> ***
>
> Info: SUMMARY OF PARAMETERS:
>
> Info: 1051 BONDS
>
> Info: 4379 ANGLES
>
> Info: 612 DIHEDRAL
>
> Info: 399 IMPROPER
>
> Info: 0 CROSSTERM
>
> Info: 108 VDW
>
> Info: 14 VDW_PAIRS
>
> Warning: VDW TYPE NAME NP MATCHES PARAMETER TYPE NAME N*
>
> Warning: VDW TYPE NAME NC MATCHES PARAMETER TYPE NAME N*
>
> Warning: VDW TYPE NAME ST MATCHES PARAMETER TYPE NAME S*
>
> Warning: Residue 1 out of order in segment MOL, lookup for additional
> residues in this segment disabled.
>
>
>
> ***
>
> Info: TIME FOR READING PSF FILE: 2.698
>
> Warning: Man, tiny Elvis, that number is huge!
>
> Warning: We don't know how X-Plor represents over Z999 residues
>
> Warning: And you just tried - so we'll fake it as -55000
>
> Warning: This is reversible, but only inside this program.
>
> Info: TIME FOR READING PDB FILE: 0.437
>
> Info:
>
> Info: Reading from binary file C:\nombre.coor
>
> Info: ****************************
>
> Info: STRUCTURE SUMMARY:
>
> Info: 127011 ATOMS
>
> Info: 89678 BONDS
>
> Info: 64131 ANGLES
>
> Info: 38854 DIHEDRALS
>
> Info: 7038 IMPROPERS
>
> Info: 0 CROSSTERMS
>
> Info: 0 EXCLUSIONS
>
> Info: 4742 CONSTRAINTS
>
> Info: 381033 DEGREES OF FREEDOM
>
> Info: 44771 HYDROGEN GROUPS
>
> Info: TOTAL MASS = 779157 amu
>
> Info: TOTAL CHARGE = -0.000231652 e
>
> Info: *****************************
>
> Info:
>
> Info: Entering startup at 483.71 s, 0 MB of memory in use
>
> Info: Startup phase 0 took 0 s, 0 MB of memory in use
>
> Info: Startup phase 1 took 0.171 s, 0 MB of memory in use
>
> Info: Startup phase 2 took 0 s, 0 MB of memory in use
>
> Info: PATCH GRID IS 8 (PERIODIC) BY 12 (PERIODIC) BY 11 (PERIODIC)
>
> Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
>
> Info: nombre.vel
>
> Info: REMOVING COM VELOCITY 0.016296 -0.00786343 -0.00547567
>
> Info: LARGEST PATCH (523) HAS 5267 ATOMS
>
> Info: CREATING 21412 COMPUTE OBJECTS
>
> Info: Startup phase 3 took 0.0940001 s, 0 MB of memory in use
>
> Info: PME using 6 and 6 processors for FFT and reciprocal sum.
>
> Info: PME GRID LOCATIONS: 0 1 2 3 4 5
>
> Info: PME TRANS LOCATIONS: 0 1 2 3 4 5
>
> FATAL ERROR: Memory allocation failed on processor 4.
>
>
>
>
>
> This application has requested the Runtime to terminate it in an unusual
> way.
>
> Please contact the application's support team for more information.
>
> FATAL ERROR: Memory allocation failed on processor 5.
>
> Program finished.
>
> FATAL ERROR: Memory allocation failed on processor 2.
>
> ------------- Processor 4 Exiting: Called CmiAbort ------------
>
> Reason: FATAL ERROR: Memory allocation failed on processor 4.
>
>
>
> --
> * mari *
>
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