Dear all,
I am now trying do NAMD simulation of proteins with amber field field. The systems crash rapidly after several dozens of minimization steps. Three chains of the proteins break down apart and run out of the water box. The program stops just when the minimization and initiation of heating, and "ERROR: Constraint failure in RATTLE algorithm for atom......" appears. The discussion about RATTLE algorithm is very common on web, I have tried many suggestions put up in these disscusions, such as desceasing the timestep, increasing margin, and increasing the temperature gradurally during heating, but none of them works.
I prepared the amberparm files, filename.crd and filename.top by tleap using the follow leap.in script:
source leaprc.ff03.r1complex = loadpdb complex_mod.pdbbond complex.101.SG complex.164.SGbond complex.203.SG complex.259.SGbond complex.300.SG complex.355.SGsavepdb complex complex1.pdbsolvateBox complex TIP3PBOX 12.0 0.75 addIons2 complex Na+ 0 saveamberparm complex complex_wb1.top complex_wb1.crd
savepdb complex complex_wb.pdb quit
And the NAMD configure file is as follow:
############################################################# ## JOB DESCRIPTION ## ############################################################# # Minimization and Equilibration of # H2PA in a Water Box ############################################################# ## ADJUSTABLE PARAMETERS ## ############################################################# amber onparmfile complex_wb.top ambercoor complex_wb.crd set temperature 310 set outputname eq1_o firsttimestep 0 ############################################################# ## SIMULATION PARAMETERS ## ############################################################# # Input #paraTypeCharmm on #parameters par_all27_prot_lipid.inp temperature $temperature # Force-Field Parameters exclude scaled1-4 1-4scaling 1.0 cutoff 12.0 switching on switchdist 10.0 pairlistdist 14.0 # Integrator Parameters timestep 2 ;# 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 86.1 0.0 0.0 cellBasisVector2 0.0 80.1 0.0 cellBasisVector3 0.0 0.0 81.3 cellOrigin 0.08574733138084412 0.287835955619812 0.16694538295269012 wrapAll onmargin 3 # PME (for full-system periodic electrostatics) PME yes PMEGridSpacing 1.0 #manual grid definition PMEGridSizeX 90 PMEGridSizeY 90 PMEGridSizeZ 90 # 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 langevinPistonDecay 50 langevinPistonTemp $temperature #Harmonic constrain if {1} { constraints on consref constr.pdb conskfile constr.pdb conskcol B constraintscaling 10.0 } # Output outputName $outputname restartfreq 500 ;# 500steps = every 1ps dcdfreq 1000 xstFreq 1000 outputEnergies 1000 outputPressure 1000 ############################################################# ## EXTRA PARAMETERS ## ############################################################# ############################################################# ## EXECUTION SCRIPT ## ############################################################# # Minimization if {1} { minimize 5000reinitvels $temperature }#Raising temperaturefor { set TEMP 10 } { $TEMP <= 300} { incr TEMP 5 } {langevinTemp $TEMPoutput md.$TEMPrun 500 ; # 2ps } run 500000 ;# 1000ps
The last energy output in namd log files:
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVGENERGY: 5000 132692.3181 88075.3164 9460.6170 0.0000 -158435.0636 -9999999999.9999 17717558.9656 0.0000 0.0000 -9999999999.9999 0.0000 -9999999999.9999 -9999999999.9999 0.0000 -3390108488.2031 -3390100133.8221 560694.3930 -3390108488.2031 -3390100133.8221
Could you help me with these? Thanks in advance!
Institute of Microbiology, Chinese Academy of Sciences
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Received on Sun Sep 01 2013 - 08:00:03 PDT
