From: Grace Shen (Lingling.Shen_at_bnpi.com)
Date: Thu Nov 03 2005 - 12:11:27 CST
Dear All:
Could anyone tell me what is wrong with my config file? It cannot increase
the temperature gradually from 0 to 300 K with 25K incensement every 1250
steps as I designed. It just jump from 0 to 110K at the first 2000 steps.
-----------------------------
#############################################################
## JOB DESCRIPTION ##
#############################################################
# Minimization and Equilibration of
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
structure a.psf
coordinates a.pdb
set outputname aequ
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters PARM.PRM
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 13.5
# 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 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp 300
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Output
outputName $outputname
restartfreq 1000 ;# 500steps = every 1ps
dcdfreq 250
outputEnergies 100
outputPressure 100
binaryoutput no
#protocol
temperature 0
reassignFreq 1250 ;#2.5ps
reassignTemp 0
reassignIncr 25
reassignHold 300
# constraints/Fixed
constraints on
consRef aCA.pdb
consKFile aCA.pdb
consKCol B
#############################################################
## EXTRA PARAMETERS ##
#############################################################
# Spherical boundary conditions
sphericalBC on
sphericalBCcenter 40.8352783065, 60.6294565467, -4.73496476132
sphericalBCr1 39
sphericalBCk1 10
sphericalBCexp1 2
#############################################################
## EXECUTION SCRIPT ##
#############################################################
#run 25000 ;# 50ps
#script
minimize 2000
run 25000 ;# 50ps
-------------------------------------------
-----------------The output file-------------------------
------------------------------------------
....
BRACKET: 0.000482275 1.83526 -11020.2 -1.38973 13725.6
NEW SEARCH DIRECTION
INITIAL STEP: 0.002048
GRADIENT TOLERANCE: 4.81439
PRESSURE: 1995 0 0 0 0 0 0 0 0 0
GPRESSURE: 1995 0 0 0 0 0 0 0 0 0
ENERGY: 1995 1199.2069 3080.2738 812.2423 43.7471
-96041.0415 -1636.9745 22.5088 0.0000 0.0000
-92520.0371 0.0000 -92520.0371 -92520.0371 0.0000
PRESSURE: 1996 0 0 0 0 0 0 0 0 0
GPRESSURE: 1996 0 0 0 0 0 0 0 0 0
ENERGY: 1996 1198.2132 3083.0814 812.2442 43.5036
-96048.2530 -1635.9838 22.5415 0.0000 0.0000
-92524.6529 0.0000 -92524.6529 -92524.6529 0.0000
PRESSURE: 1997 0 0 0 0 0 0 0 0 0
GPRESSURE: 1997 0 0 0 0 0 0 0 0 0
ENERGY: 1997 1199.9127 3089.4325 812.7921 47.2117
-96063.4108 -1631.6878 22.6109 0.0000 0.0000
-92523.1387 0.0000 -92523.1387 -92523.1387 0.0000
BRACKET: 0.000620019 4.61578 -30957.7 -13696.3 21083.8
PRESSURE: 1998 0 0 0 0 0 0 0 0 0
GPRESSURE: 1998 0 0 0 0 0 0 0 0 0
ENERGY: 1998 1198.2956 3085.4695 812.3739 44.2987
-96054.1152 -1634.6626 22.5683 0.0000 0.0000
-92525.7719 0.0000 -92525.7719 -92525.7719 0.0000
BRACKET: 0.000413346 2.63315 -13696.3 -19.4108 21083.8
PRESSURE: 1999 0 0 0 0 0 0 0 0 0
GPRESSURE: 1999 0 0 0 0 0 0 0 0 0
ENERGY: 1999 1198.3760 3085.8495 812.4039 44.4978
-96055.0285 -1634.4171 22.5725 0.0000 0.0000
-92525.7460 0.0000 -92525.7460 -92525.7460 0.0000
BRACKET: 0.000188089 1.11896 -13696.3 -19.4108 2084.7
PRESSURE: 2000 0 0 0 0 0 0 0 0 0
GPRESSURE: 2000 0 0 0 0 0 0 0 0 0
ETITLE: TS BOND ANGLE DIHED IMPRP
ELECT VDW BOUNDARY MISC KINETIC
TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG
ENERGY: 2000 1198.2956 3085.4695 812.3739 44.2987
-96054.1152 -1634.6626 22.5683 0.0000 0.0000
-92525.7719 0.0000 -92525.7719 -92525.7719 0.0000
WRITING COORDINATES TO DCD FILE AT STEP 2000
WRITING COORDINATES TO RESTART FILE AT STEP 2000
FINISHED WRITING RESTART COORDINATES
WRITING VELOCITIES TO RESTART FILE AT STEP 2000
FINISHED WRITING RESTART VELOCITIES
TCL: Running for 25000 steps
PRESSURE: 2000 0 0 0 0 0 0 0 0 0
GPRESSURE: 2000 0 0 0 0 0 0 0 0 0
ETITLE: TS BOND ANGLE DIHED IMPRP
ELECT VDW BOUNDARY MISC KINETIC
TOTAL TEMP TOTAL2 TOTAL3 TEMPAVG
ENERGY: 2000 200.8669 791.6991 812.3537 44.2769
-88394.6369 -2724.4570 22.8350 0.0000 0.0000
-89247.0623 0.0000 -89246.2287 -89249.3546 0.0000
Info: Initial time: 1 CPUs 0.918326 s/step 5.31439 days/ns 141512 kB memory
PRESSURE: 2100 0 0 0 0 0 0 0 0 0
GPRESSURE: 2100 0 0 0 0 0 0 0 0 0
PRESSAVG: 2100 0 0 0 0 0 0 0 0 0
GPRESSAVG: 2100 0 0 0 0 0 0 0 0 0
Info: Initial time: 1 CPUs 0.78035 s/step 4.51591 days/ns 142357 kB memory
ENERGY: 2100 627.5279 1510.7675 908.8404 136.9452
-85421.7387 -2610.0566 29.8795 0.0000 5907.0107
-78910.8242 115.7239 -78900.3341 -78924.0470 71.1123
Info: Initial time: 1 CPUs 0.78188 s/step 4.52477 days/ns 142732 kB memory
PRESSURE: 2200 0 0 0 0 0 0 0 0 0
GPRESSURE: 2200 0 0 0 0 0 0 0 0 0
PRESSAVG: 2200 0 0 0 0 0 0 0 0 0
GPRESSAVG: 2200 0 0 0 0 0 0 0 0 0
Info: Benchmark time: 1 CPUs 0.783469 s/step 4.53397 days/ns 143029 kB
memory
ENERGY: 2200 760.1043 1965.8890 989.8897 191.6956
-82987.6245 -2826.5591 38.3782 0.0000 8748.8243
-73119.4026 171.3978 -73093.7851 -73100.0035 146.1213
Info: Benchmark time: 1 CPUs 0.769777 s/step 4.45473 days/ns 143716 kB
memory
WRITING COORDINATES TO DCD FILE AT STEP 2250
PRESSURE: 2300 0 0 0 0 0 0 0 0 0
GPRESSURE: 2300 0 0 0 0 0 0 0 0 0
PRESSAVG: 2300 0 0 0 0 0 0 0 0 0
GPRESSAVG: 2300 0 0 0 0 0 0 0 0 0
Info: Benchmark time: 1 CPUs 0.771563 s/step 4.46506 days/ns 143962 kB
memory
ENERGY: 2300 847.2974 2172.0799 1043.3795 228.3438
-81278.6578 -3148.0061 42.0292 0.0000 10807.5127
-69286.0216 211.7294 -69246.0089 -69259.1053 193.3866
PRESSURE: 2400 0 0 0 0 0 0 0 0 0
GPRESSURE: 2400 0 0 0 0 0 0 0 0 0
PRESSAVG: 2400 0 0 0 0 0 0 0 0 0
GPRESSAVG: 2400 0 0 0 0 0 0 0 0 0
ENERGY: 2400 943.7482 2353.7187 1059.9316 238.2200
-79958.3569 -3429.3480 49.5715 0.0000 12155.3210
-66587.1939 238.1343 -66541.0084 -66542.6397 224.2667
REASSIGNING VELOCITIES AT STEP 2500 TO 50 KELVIN.
PRESSURE: 2500 0 0 0 0 0 0 0 0 0
GPRESSURE: 2500 0 0 0 0 0 0 0 0 0
PRESSAVG: 2500 0 0 0 0 0 0 0 0 0
GPRESSAVG: 2500 0 0 0 0 0 0 0 0 0
ENERGY: 2500 966.2761 2433.6132 1066.0587 233.3577
-79241.6444 -3481.9979 44.8798 0.0000 2681.3252
-75298.1316 52.5297 -73527.2587 -79971.6984 244.0770
WRITING COORDINATES TO DCD FILE AT STEP 2500
PRESSURE: 2600 0 0 0 0 0 0 0 0 0
GPRESSURE: 2600 0 0 0 0 0 0 0 0 0
PRESSAVG: 2600 0 0 0 0 0 0 0 0 0
GPRESSAVG: 2600 0 0 0 0 0 0 0 0 0
ENERGY: 2600 827.0634 2105.9077 982.7922 198.2737
-81504.1616 -3659.1649 43.9969 0.0000 10806.5033
-70198.7894 211.7096 -70161.0855 -70165.6605 184.8769
PRESSURE: 2700 0 0 0 0 0 0 0 0 0
GPRESSURE: 2700 0 0 0 0 0 0 0 0 0
PRESSAVG: 2700 0 0 0 0 0 0 0 0 0
GPRESSAVG: 2700 0 0 0 0 0 0 0 0 0
ENERGY: 2700 926.1251 2318.2219 1024.4083 225.2323
-80272.1284 -3711.4737 51.5941 0.0000 12156.3118
-67281.7084 238.1537 -67231.9878 -67247.0664 226.0864
WRITING COORDINATES TO DCD FILE AT STEP 2750
PRESSURE: 2800 0 0 0 0 0 0 0 0 0
GPRESSURE: 2800 0 0 0 0 0 0 0 0 0
PRESSAVG: 2800 0 0 0 0 0 0 0 0 0
GPRESSAVG: 2800 0 0 0 0 0 0 0 0 0
ENERGY: 2800 990.2192 2449.6426 1057.6643 225.1925
-79437.2204 -3842.5558 57.6183 0.0000 13118.5888
-65380.8504 257.0056 -65325.8317 -65332.5169 249.0013
PRESSURE: 2900 0 0 0 0 0 0 0 0 0
GPRESSURE: 2900 0 0 0 0 0 0 0 0 0
PRESSAVG: 2900 0 0 0 0 0 0 0 0 0
GPRESSAVG: 2900 0 0 0 0 0 0 0 0 0
ENERGY: 2900 972.9754 2563.7909 1058.0721 252.2182
-78574.5729 -4119.1125 59.5664 0.0000 13738.0276
-64049.0347 269.1410 -63990.2750 -63993.7388 264.1499
...........
....
----------------------------
---------------------------
Thanks
Grace
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