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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