Re: Constraint failure in RATTLE algorithm occurs during NAMD simulation with amber force field

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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