From: juan jesus sanchez sanchez (pibaneo_at_hotmail.es)
Date: Wed May 18 2011 - 12:32:09 CDT

hi to all, first of all im new on this whole world of NAMD and VMD
and also my english is not so good as i wish.

well the problem starts when i try to merge two identical proteins
to do this i write the follows commands in tk console:
(xoq and xoq1 are the names of my proteins)

mol new xoq.psf

mol addfile xoq.pdb

mol new xoq1.psf

mol addfile xoq1.pdb

set sel [atomselect top all]

$sel moveby {20 0 0 }

when displays in vmd opengl dislplay i can see the two proteins separates by 20A
but when i use the command ¨merge structures¨ and try to see the pfs and pdb
archives generated with merge structures i only see one protein in vmd opengl display
i dont know if this is correct or iam doing something wrong?. I check the psf and pdb
archives in a text editor, in there i see the two identical proteins but no in vdm opengl display

Also when i run the simulation after one week i receive the following error message:

ERROR: Constraint failure in RATTLE algorithm for atom 1486!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Atom 1501 velocity is 71332.2 -56031.1 103630 (limit is 12000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Exiting prematurely; see error messages above.
====================================================

and after 2 weeks of run the same simulation this error message:
The last position output (seq=8940750) takes 0.001 seconds, 10109.280 MB of memory in use
ERROR: Atom 12088 velocity is nan nan nan (limit is 24000)
ERROR: Atom 12089 velocity is nan nan nan (limit is 24000)
ERROR: Atom 12090 velocity is nan nan nan (limit is 24000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Atom 4711 velocity is nan nan nan (limit is 24000)
ERROR: Atom 4712 velocity is nan nan nan (limit is 24000)
ERROR: Atom 4713 velocity is nan nan nan (limit is 24000)
ERROR: Atoms moving too fast; simulation has become unstable.
ERROR: Exiting prematurely; see error messages above.
====================================================

this is the info of my simulation:
Charm++: scheduler running in netpoll mode.
Charm++> Running on 1 unique compute nodes (4-way SMP).
Charm++> Cpu topology info:
PE to node map: 0 0
Node to PE map:
Chip #0: 0 1
Charm++> cpu topology info is gathered in 0.006 seconds.
Info: NAMD CVS for Linux-x86_64
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 Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 60202 for net-linux-x86_64
Info: Built Fri Feb 4 08:09:39 CST 2011 by root on THeHaRd
Info: 1 NAMD CVS Linux-x86_64 2 THeHaRd root
Info: Running on 2 processors.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.00812602 s
Info: 1.63802 MB of memory in use based on CmiMemoryUsage
Info: Changed directory to namd-tutorial-files/1-2-sphere
Info: Configuration file is newxoq_ws_eq.conf
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 0.5
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 100
Info: LOAD BALANCER Centralized
Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT
Info: LDB PERIOD 20000 steps
Info: FIRST LDB TIMESTEP 500
Info: LAST LDB TIMESTEP -1
Info: LDB BACKGROUND SCALING 1
Info: HOM 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: INITIAL TEMPERATURE 310
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 ELECTROSTATICS SCALED BY 1
Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED
Info: DCD FILENAME newxoq_ws_eqv5.dcd
Info: DCD FREQUENCY 250
Info: DCD FIRST STEP 250
Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME newxoq_ws_eqv5
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME newxoq_ws_eqv5.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: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 1000
Info: PRESSURE OUTPUT STEPS 100
Info: SPHERICAL BOUNDARY CONDITIONS ACTIVE
Info: RADIUS #1 37.1313
Info: FORCE CONSTANT #1 10
Info: EXPONENT #1 2
Info: SPHERE BOUNDARY CENTER(-0.0635865, -0.566768, 0.536454)
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 1304074838
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB ../common/newxoq_ws.pdb
Info: STRUCTURE FILE ../common/newxoq_ws.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS ../common/par_all27_prot_lipid.inp
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SUMMARY OF PARAMETERS:
Info: 180 BONDS
Info: 447 ANGLES
Info: 566 DIHEDRAL
Info: 46 IMPROPER
Info: 6 CROSSTERM
Info: 119 VDW
Info: 0 VDW_PAIRS
Info: TIME FOR READING PSF FILE: 0.204903
Info: TIME FOR READING PDB FILE: 0.041837
Info:
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 20856 ATOMS
Info: 15524 BONDS
Info: 14076 ANGLES
Info: 12774 DIHEDRALS
Info: 710 IMPROPERS
Info: 298 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 18522 RIGID BONDS
Info: 44046 DEGREES OF FREEDOM
Info: 7718 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 7718 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 130067 amu
Info: TOTAL CHARGE = -14 e
Info: *****************************
Info:
Info: Entering startup at 0.273826 s, 7.44449 MB of memory in use
Info: Startup phase 0 took 0.000674963 s, 7.43967 MB of memory in use
Info: Startup phase 1 took 0.0888009 s, 11.313 MB of memory in use
Info: Startup phase 2 took 0.000277996 s, 11.4755 MB of memory in use
Info: Startup phase 3 took 8.60691e-05 s, 11.476 MB of memory in use
Info: PATCH GRID IS 4 BY 4 BY 4
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: REMOVING COM VELOCITY -0.0167083 0.00621663 -0.0331727
Info: LARGEST PATCH (43) HAS 641 ATOMS
Info: Startup phase 4 took 0.0191739 s, 14.57 MB of memory in use
Info: Startup phase 5 took 0.000203133 s, 14.5675 MB of memory in use
Info: Startup phase 6 took 0.00247788 s, 13.087 MB of memory in use
LDB: Central LB being created...
Info: Startup phase 7 took 1.2 s, 13.0643 MB of memory in use
Info: CREATING 1114 COMPUTE OBJECTS
Info: useSync: 1 useProxySync: 0
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: Startup phase 8 took 0.0045979 s, 15.5538 MB of memory in use
Info: Startup phase 9 took 0.000298977 s, 19.7175 MB of memory in use
Info: Finished startup at 1.59042 s, 19.7175 MB of memory in use

hope someone can helpme

Thanks!!!

Juan Sanchez