RE: Simulation continuously crashes after minimization

From: Cruz-Chu Eduardo Roberto (eduardo.cruz_at_mavt.ethz.ch)
Date: Tue Feb 12 2013 - 17:00:57 CST

remove the water or use implicit solvent.

________________________________
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of Patricia Campbell [patricia.campbellsoup_at_gmail.com]
Sent: Tuesday, February 12, 2013 10:01 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: Simulation continuously crashes after minimization

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<tel: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<tel:706-577-3754>
patricia.campbellsoup_at_gmail.com<mailto:patricia.campbellsoup_at_gmail.com>

This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:20:55 CST