Problem with NAMD and constraint failures

From: rwiese_at_unr.edu
Date: Thu Jan 19 2006 - 18:27:11 CST

Hi.

I am a new user of NAMD, and am having a problem setting up a simulation.

I built a POPE layer and placed a GRO-alpha molecule above it. I then
solvated the top area and calculated the periodic box dimensions. I set
up a conf file for this.

When I run NAMD, I get this:

---
Charm++: standalone mode (not using charmrun)
Info: NAMD 2.6b1 for Linux-amd64
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
Info:
Info: Please cite Kale et al., J. Comp. Phys. 151:283-312 (1999)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 50900 for net-linux-amd64-iccstatic
Info: Built Fri Jul 29 11:31:55 CDT 2005 by jim on tijuana.ks.uiuc.edu
Info: Sending usage information to NAMD developers via UDP.  Sent data is:
Info: 1 NAMD  2.6b1  Linux-amd64  1    rottie  wiese
Info: Running on 1 processors.
Info: 8097 kB of memory in use.
Info: Configuration file is groa_mem_solv.conf
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP               2
Info: NUMBER OF STEPS        0
Info: STEPS PER CYCLE        10
Info: LOAD BALANCE STRATEGY  Other
Info: LDB PERIOD             2000 steps
Info: FIRST LDB TIMESTEP     50
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: MAX SELF PARTITIONS    50
Info: MAX PAIR PARTITIONS    20
Info: SELF PARTITION ATOMS   125
Info: PAIR PARTITION ATOMS   200
Info: PAIR2 PARTITION ATOMS  400
Info: MIN ATOMS PER PATCH    100
Info: INITIAL TEMPERATURE    310
Info: CENTER OF MASS MOVING? NO
Info: DIELECTRIC             1
Info: EXCLUDE                SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR       1
Info: DCD FILENAME           groamemsolv_dyn.dcd
Info: DCD FREQUENCY          500
Info: DCD FIRST STEP         500
Info: XST FILENAME           groamemsolv_dyn.xst
Info: XST FREQUENCY          500
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME        groamemsolv_dyn
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME       groamemsolv_dyn.restart
Info: RESTART FREQUENCY      500
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON           10
Info: SWITCHING OFF          12
Info: PAIRLIST DISTANCE      13.5
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        16
Info: ENERGY OUTPUT STEPS    100
Info: PRESSURE OUTPUT STEPS  100
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE   310
Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RIGID BONDS TO HYDROGEN : ALL
Info:         ERROR TOLERANCE : 1e-08
Info:          MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBER SEED     1137703119
Info: USE HYDROGEN BONDS?    NO
Info: COORDINATE PDB         groa_mem_solv.pdb
Info: STRUCTURE FILE         groa_mem_solv.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS             par_all27_prot_lipid.inp
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SUMMARY OF PARAMETERS:
Info: 179 BONDS
Info: 441 ANGLES
Info: 534 DIHEDRAL
Info: 49 IMPROPER
Info: 89 VDW
Info: 0 VDW_PAIRS
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 98047 ATOMS
Info: 77700 BONDS
Info: 92240 ANGLES
Info: 100490 DIHEDRALS
Info: 745 IMPROPERS
Info: 0 EXCLUSIONS
Info: 83271 RIGID BONDS
Info: 210870 DEGREES OF FREEDOM
Info: 34855 HYDROGEN GROUPS
Info: TOTAL MASS = 577596 amu
Info: TOTAL CHARGE = 6.00004 e
Info: *****************************
Info: Entering startup phase 0 with 55254 kB of memory in use.
Info: Entering startup phase 1 with 55255 kB of memory in use.
Info: Entering startup phase 2 with 93895 kB of memory in use.
Info: Entering startup phase 3 with 94663 kB of memory in use.
Info: PATCH GRID IS 7 BY 7 BY 7
Info: REMOVING COM VELOCITY -0.00301731 0.0299689 0.00751947
Info: LARGEST PATCH (122) HAS 451 ATOMS
Info: Entering startup phase 4 with 118775 kB of memory in use.
Info: Entering startup phase 5 with 118775 kB of memory in use.
Info: Entering startup phase 6 with 118775 kB of memory in use.
Measuring processor speeds... Done.
Info: Entering startup phase 7 with 118776 kB of memory in use.
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 1.69407e-21 AT 11.9974
Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 1.13046e-16 AT 11.9974
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 2 AT 0.0441942
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 1.26461e-15 AT 0.0441942
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 16384 AT 0.0441942
Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 5.05845e-15 AT 0.0441942
Info: Entering startup phase 8 with 138028 kB of memory in use.
Info: Finished startup with 226182 kB of memory in use.
TCL: Running for 50000 steps
ERROR: Constraint failure in RATTLE algorithm for atom 14901!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 36367!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 14485!
ERROR: Constraint failure; simulation has become unstable.
(there are a lot more Constraint failure atoms)
---
Can anyone explain what is going on?
I can send the setup files if that would help.
Robert Wiese
UNR

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