From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Fri Jan 20 2006 - 01:00:55 CST
Hello Robert
The problem is you didn't say if you have minimized or
equilibrated the
system. Taking a nonequilibrated system and not slowly heating to 310K
will tend to rip hydrogen atoms off their heavy atom partners. Rattle
will fail.
A quick search through the list will reveal the answer to this question as
well as the namd wiki.
Regards
Brian
wrote:
> 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
>
************************************************
Brian Bennion, Ph.D.
Bioscience Directorate
Lawrence Livermore National Laboratory
P.O. Box 808, L-448 bennion1_at_llnl.gov
7000 East Avenue phone: (925) 422-5722
Livermore, CA 94550 fax: (925) 424-6605
************************************************
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