From: Urszula Uciechowska (urszula.uciechowska_at_biotech.ug.edu.pl)
Date: Tue Feb 03 2015 - 08:23:28 CST
Dear namd users,
I want to run MD simulations of the DNA-protein complex. During the
minimization I am getting an error message:
RESSURE: 99 10731.6 191.359 769.037 191.359 11866.8 -117.473 769.037
-117.473 11668.2
GPRESSURE: 99 13089.3 233.036 1070.8 170.059 13957.7 -328.039 1217.48
-37.0102 13888
ENERGY: 99 37247.5702 16922.0187 4534.2241
211.6177 -404403.0066 89202.3123 0.0000 0.0000
0.0000 -256285.2636 0.0000 -256285.2636
-256285.2636 0.0000 11422.2056 13644.9963
1157625.0000 11422.2056 13644.9963
LDB: ============= START OF LOAD BALANCING ============== 50.2813
LDB: Largest compute 34 load 0.297668 is 6.8% of average load 4.379461
LDB: Average compute 0.036585 is 0.8% of average load 4.379461
LDB: TIME 50.2822 LOAD: AVG 4.37946 MAX 5.40094 PROXIES: TOTAL 427 MAXPE
20 MAXPATCH 6 None MEM: 176.457 MB
LDB: TIME 50.2841 LOAD: AVG 4.37946 MAX 4.58958 PROXIES: TOTAL 427 MAXPE
20 MAXPATCH 6 TorusLB MEM: 176.457 MB
LDB: ============== END OF LOAD BALANCING =============== 50.3
Info: useSync: 1 useProxySync: 0
LDB: =============== DONE WITH MIGRATION ================ 50.3354
PRESSURE: 100 10731.6 191.359 769.037 191.359 11866.8 -117.473 769.037
-117.473 11668.2
GPRESSURE: 100 13089.3 233.037 1070.8 170.059 13957.7 -328.039 1217.48
-37.0102 13888
Info: Initial time: 24 CPUs 0.134836 s/step 0.780302 days/ns 176.457 MB
memory
ETITLE: TS BOND ANGLE DIHED
IMPRP ELECT VDW BOUNDARY MISC
KINETIC TOTAL TEMP POTENTIAL
TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME
PRESSAVG GPRESSAVG
ENERGY: 100 37247.5702 16922.0187 4534.2241
211.6177 -404403.0063 89202.3123 0.0000 0.0000
0.0000 -256285.2633 0.0000 -256285.2633
-256285.2633 0.0000 11422.2056 13644.9963
1157625.0000 11422.2056 13644.9963
REINITIALIZING VELOCITIES AT STEP 100 TO 310 KELVIN.
TCL: Running for 8000 steps
ERROR: Constraint failure in RATTLE algorithm for atom 1460!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 270!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Constraint failure in RATTLE algorithm for atom 532!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely; see error messages above.
====================================================
the input file was:
#############################################################
## JOB DESCRIPTION ##
#############################################################
# Minimization and Equilibration of
# Ubiquitin in a Water Box
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure ssb.psf
coordinates ssb.pdb
set temperature 310
set outputname ssb_wb_eq
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters par_all36_na.prm
parameters par_all36_prot.prm
parameters par_water_ions_na.prm
temperature $temperature
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 14
switching on
switchdist 10.0
pairlistdist 16.0
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 1/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Periodic Boundary Conditions
cellBasisVector1 105.0 0. 0.0
cellBasisVector2 0.0 105.0 0.0
cellBasisVector3 0.0 0 105.0
cellOrigin 51.7 51.8 49.6
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSpacing 1.0
#manual grid definition
#PMEGridSizeX 45
#PMEGridSizeY 45
#PMEGridSizeZ 48
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigidBonds
useFlexibleCell no
useConstantArea no
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 100.0
langevinPistonDecay 50.0
langevinPistonTemp $temperature
# Output
outputName $outputname
restartfreq 500 ;# 500steps = every 1ps
dcdfreq 250
xstFreq 250
outputEnergies 100
outputPressure 100
#############################################################
## EXTRA PARAMETERS ##
#############################################################
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 100
reinitvels $temperature
run 8000 ;# 5ps
What can be wrong here? I did not have any errors during psfgn preparation.
Please suggest.
Thanks for any suggestion
Best regards
Urszula Uciechowska
University of Gdansk and Medical Univesity of Gdansk
Department of Molecular and Cellular Biology
ul. Kladki 24
80-822 Gdansk
Poland
-----------------------------------------
Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego
http://www.ug.edu.pl/
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