Simulation continuously crashes after minimization

From: Patricia Campbell (patricia.campbellsoup_at_gmail.com)
Date: Tue Feb 12 2013 - 14:52:03 CST

My goal is to fit a rather large protein structure into a Cryo-EM density
map and I have been following the MDFF tutorials to do that. I have been
trying to run a simulation in a solvation box that always crashes at the
first step of the simulation. I have tried the following

   - Checked to see if I could run the simulation with fewer
   proteins (I could but now I need a larger scale simulation)
   - Made sure the target density map sits inside the solvation box
   as well as made the box bigger so that no atoms are too close to the edge
   - Not using a structure that is a the result of another NAMD
   simulation
   - Refitting the crystal structure into the density map
   - Mutating a particularly stubborn residue to an alanine
   - Running the simulation on two different systems
      - o CPU: Intel core i7-3820; GPU: NVIDIA GTX 690
      - o CPU: 2x2.66 GHz Dual-Core Intel Xeon; NVIDIA GeForce GTX 470
      1280 MB
   - Changing the number of minimization steps (started at 200 steps)
      - o 2000 steps
      - o 4000 steps
   - Starting at a lower temperature
      - o Starting temp of 100K with a final temp of 300K
   - Increasing the margin value
   - Choosing to add ions to the system either by
      - o only neutralize the system with NaCl
      - o NaCl concentration at 150 mM/L

All have had error messages that look like the following:

ENERGY: 2000 20045.3695 28655.9242 14964.8238
3061.5794 -3989765.5672 -9999999999.9999 0.0000
69807.4435 678617.7419 -9999999999.9999 300.2457
-9999999999.9999 -9999999999.9999 300.2457 -22194.2416
-2352.0620 11521006.9573 -22194.2416 -2352.0620

ERROR: Atom 13407 velocity is 9683.62 -9253.66 -4407.55 (limit is 10000,
atom 27 of 376 on patch 1912 pe 0)

ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on
patch 1912 pe 0).

ERROR: Exiting prematurely; see error messages above.

TCL: Running for 100000 steps

PRESSURE: 200 -22430.7 -26.3417 -69.5681 -19.5908 -22647.5 190.443 -93.526
227.535 -22632.6

GPRESSURE: 200 -2683.59 102.214 89.1581 9.15734 -2815.47 13.9541 27.7538
148.065 -2470.87

ENERGY: 200 7036.1969 23982.6941 13678.0172
2385.4084 -4018992.1551 288584.1172 0.0000
69809.8812 677965.3746 -2935550.4655 299.9570
-3613515.8402 -2939335.0168 299.9570 -22570.2667
-2656.6453 11521006.9573 -22570.2667 -2656.6453

ERROR: Atom 13353 velocity is -345013 286249 179665 (limit is 10000, atom
52 of 215 on patch 2778 pe 0)

ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on
patch 2778 pe 0).

ERROR: Atom 13357 velocity is 26452 -22404.1 -19947.7 (limit is 10000, atom
267 of 268 on patch 3002 pe 0)

ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on
patch 3002 pe 0).

ERROR: Exiting prematurely; see error messages above.

====================================================

So on and so forth. I have also had a bad global exclusion count on one or
two of the simulations but not all. I am wondering if there is something
very obvious here that I am missing. I have tried taring up a sample of my
files but get error messages from your email service. Please let me know if
there is a way to send files that you need to understand what is going on.

example of one namd file that failed:

### Docking -- Step 1

set PSFFILE ionized.psf

set PDBFILE ionized.pdb

set GRIDPDB ion-grid.pdb

set DIEL 1

set SCALING_1_4 1.0

set ITEMP 300

set FTEMP 300

set GRIDFILE nonNAMDcootmap-grid.dx

set GSCALE 0.3

set EXTRAB {ion-extrabonds.txt ion-cispeptide.txt ion-chirality.txt}

set CONSPDB 0

set FIXPDB 0

set OUTPUTNAME adk-solvent-step1

set TS 100000

set MS 200

set MARGIN 0

####################################

structure $PSFFILE

coordinates $PDBFILE

paraTypeCharmm on

parameters par_all27_prot_lipid_na.inp

if {[info exists INPUTNAME]} {

  BinVelocities $INPUTNAME.restart.vel

  BinCoordinates $INPUTNAME.restart.coor

  ExtendedSystem $INPUTNAME.restart.xsc

} else {

  temperature $ITEMP

  cellBasisVector1 249.33098602294922 0 0

  cellBasisVector2 0 227.7590103149414 0

  cellBasisVector3 0 0 298.8009948730469

  cellOrigin -157.66326904296875 -186.63685607910156 -68.98925018310547

}

PME yes

PMEGridSpacing 1.0

PMEPencils 1

wrapAll on

source mdff_template.namd

-- 
Patricia Campbell
706-577-3754
patricia.campbellsoup_at_gmail.com
-- 
Patricia Campbell
706-577-3754
patricia.campbellsoup_at_gmail.com

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