From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Thu Aug 29 2013 - 22:58:38 CDT
You have huge forces in your system. So, something in the system setup is
wrong rather than in the parameter files. Probably, you might have
clashing atoms or your specified box dimensions are smaller than the box
you created.
Gianluca
On Fri, 30 Aug 2013, sunyeping wrote:
> 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.r1
> complex = loadpdb complex_mod.pdb
> bond complex.101.SG complex.164.SG
> bond complex.203.SG complex.259.SG
> bond complex.300.SG complex.355.SG
> savepdb complex complex1.pdb
> solvateBox 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 on
> parmfile 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 on
> margin 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 5000
> reinitvels $temperature
> }
>
> #Raising temperature
> for { set TEMP 10 } { $TEMP <= 300} { incr TEMP 5 } {
> langevinTemp $TEMP
> output md.$TEMP
> run 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 GPRESSAVG
>
> ENERGY: 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
>
> Institute of Microbiology, Chinese Academy of Sciences
>
>
>
-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
+1 (206) 685 4435
http://artemide.bioeng.washington.edu/
Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
http://healthynaturalbaby.org
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