Tutorial-l Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Mar 23 2012 - 09:36:16 CDT

You made a mistake setting up your system, such that there are clashes, i.e., overlapping atoms, that can not be fixed. Look at your system, particularly the region around those atoms noted in the log file (remember to use "serial" and not "index" in VMD!) to figure out what went wrong.

On Mar 22, 2012, at 9:27 AM, Albert wrote:

> Hello:
> I am following the membrane protein simulation protocol and I am trying to equilibrium the system by following input file:
>
>
> #############################################################
> ## JOB DESCRIPTION ##
> #############################################################
>
> # Min. and Eq. of protein
> # embedded in POPC membrane, ions and water.
> # Melting lipid tails. PME, Constant Volume.
>
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
>
> structure ../step5_assembly.xplor.psf
> coordinates ../step5_assembly.pdb
> outputName popcwimineq-01
>
> set temperature 310
>
> # Continuing a job from the restart files
> if {0} {
> set inputname assembly
> binCoordinates $inputname.restart.coor
> binVelocities $inputname.restart.vel ;# remove the "temperature" entry if you use this!
> extendedSystem $inputname.restart.xsc
> }
>
> firsttimestep 0
>
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters ../toppar/par_all22_prot.prm;
> parameters ../toppar/par_all27_na.prm;
> parameters ../toppar/par_all36_carb.prm;
> parameters ../toppar/par_all36_lipid.prm;
> #parameters ../toppar/par_all36_cgenff.prm;
> parameters ../toppar/par_all27_prot_lipidNBFIX.prm
> #parameters ../toppar/toppar_water_ions.str;
> #parameters ../toppar/toppar_all36_lipid_cholesterol.str;
>
>
> # NOTE: Do not set the initial velocity temperature if you
> # have also specified a .vel restart file!
> temperature $temperature
>
>
> # Periodic Boundary conditions. Need this since for a start...
> cellBasisVector1 76.6 0.0 0.0; # vector to the next image
> cellBasisVector2 0.0 76.6 0.0;
> cellBasisVector3 0.0 0.0 105.4;
> cellOrigin 0.0 0.0 0.0; # the *center* of the cell
>
> wrapWater on; # wrap water to central cell
> wrapAll on; # wrap other molecules too
> wrapNearest off; # use for non-rectangular cells (wrap to the nearest image)
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 10.
> pairlistdist 13.5
>
>
> # Integrator Parameters
> timestep 1.0 ;# 1fs/step
> rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 20
>
>
> #PME (for full-system periodic electrostatics)
> if {1} {
> PME yes
> PMEGridSizeX 80
> PMEGridSizeY 80
> PMEGridSizeZ 90
> }
>
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
>
> # Constant Pressure Control (variable volume)
> if {0} {
> useGroupPressure yes ;# needed for 2fs steps
> useFlexibleCell yes ;# no for water box, yes for membrane
> useConstantArea no ;# no for water box, yes for membrane
>
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 200.
> langevinPistonDecay 50.
> langevinPistonTemp $temperature
> }
>
>
> restartfreq 1000 ;# 1000steps = every 2ps
> dcdfreq 1000
> xstFreq 1000
> outputEnergies 50
> outputPressure 50
>
>
> # Fixed Atoms Constraint (set PDB beta-column to 1)
> if {1} {
> fixedAtoms on
> fixedAtomsFile ../fix_prot.pdb
> fixedAtomsCol B
> fixedAtomsForces on
> }
>
> #############################################################
> ## EXTRA PARAMETERS ##
> #############################################################
>
> # Put here any custom parameters that are specific to
> # this job (e.g., SMD, TclForces, etc...)
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Minimization
> if {1} {
> minimize 1000
> reinitvels $temperature
> }
>
> run 500000 ;# 0.5 ns
>
>
>
>
> But, it said:
>
> LINE MINIMIZER BRACKET: DX 0 2.6857e-116 DU 0 0.000976562 DUDX -6.99825e+11 -6.99825e+11 -6.99328e+11
> PRESSURE: 1000 2.44943e+08 -15852.3 -8789.58 -1.22401e+08 57042.6 13168.1 -7.04417e+07 10762.6 47620.3
> GPRESSURE: 1000 2.44976e+08 -21451.9 10739 -1.22399e+08 56236.4 14020.2 -7.04015e+07 2695.95 69875.7
> Warning: Energy evaluation is expensive, increase outputEnergies to improve performance.
> TIMING: 1000 CPU: 31.7652, 0.0319331/step Wall: 32.1639, 0.0321847/step, 0 hours remaining, 242.742188 MB of memory in use.
> ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
>
> ENERGY: 1000 39338.0170 79155.4220 10358.6830 296.6790 -145462.9569 -9999999999.9999 0.0000 0.0000 0.0000 -9999999999.9999 0.0000 -9999999999.9999 -9999999999.9999 0.0000 81682598.3462 81700597.5419 618440.8240 81682598.3462 81700597.5419
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 1000
> OPENING COORDINATE DCD FILE
> WRITING COORDINATES TO DCD FILE AT STEP 1000
> WRITING COORDINATES TO RESTART FILE AT STEP 1000
> FINISHED WRITING RESTART COORDINATES
> The last position output (seq=1000) takes 0.004 seconds, 242.945 MB of memory in use
> WRITING VELOCITIES TO RESTART FILE AT STEP 1000
> FINISHED WRITING RESTART VELOCITIES
> The last velocity output (seq=1000) takes 0.001 seconds, 242.586 MB of memory in use
> REINITIALIZING VELOCITIES AT STEP 1000 TO 310 KELVIN.
> TCL: Running for 500000 steps
> ERROR: Constraint failure in RATTLE algorithm for atom 15029!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Constraint failure in RATTLE algorithm for atom 7201!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Constraint failure in RATTLE algorithm for atom 5436!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Exiting prematurely; see error messages above.
> ====================================================
>
> WallClock: 57.276257 CPUTime: 55.389580 Memory: 243.140625 MB
>

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