VMD-L Mailing List

From: Joshua Adelman (jla65_at_pitt.edu)
Date: Fri May 21 2010 - 07:56:06 CDT

Hi Prija,

If you take a look at the NAMD wiki, you'll find that your exact problem and possible solutions are detailed there (along with numerous previous posts to the list):
http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdTroubleshooting

That said, looking at the original configuration file from the tutorial, (at least in the version I found online), it specifies doing 1000 steps of minimization, not 100 as you have below. 100 steps of minimization is rarely enough to remove bad contacts (depending on the quality of your initial structure), and there are much more gentle ways to prepare a system, such as gradually heating it and using restraints to relax different parts of your system 'separately'.

You should note that in general, the tutorials use protocols that are meant for computational expediency, and are not generally how you would want to do things if you were attempting to do a production grade simulation.

Best of luck,
Josh

On May 21, 2010, at 6:24 AM, Prija Ponnan wrote:

> Hello
> I have run simulation of GST as given in the "topology tutorial"
> the configuration file is as follows
>
> #############################################################
> ## JOB DESCRIPTION ##
> #############################################################
>
> # Minimization and Equilibration of
> # Human Pi GST in a Water Box
> # N, V, E simulation
>
>
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
>
> structure gst_solv_ion.psf
> coordinates gst_solv_ion.pdb
>
> set temperature 298
> set outputname gst_wb_mineq
>
> 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.
> switching on
> switchdist 10.
> pairlistdist 14.0
>
>
> # Integrator Parameters
> timestep 1.0 ;# 2fs/step
> #rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
> langevinTemp $temperature
> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>
>
> # Periodic Boundary Conditions
> cellBasisVector1 58.9 0. 0.
> cellBasisVector2 0. 76.7 0.
> cellBasisVector3 0. 0 68.2
> cellOrigin 17.7 12.4 15.8
>
> wrapAll on
>
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 64
> PMEGridSizeY 80
> PMEGridSizeZ 74
>
> # Output
> outputName $outputname
>
> restartfreq 1000 ;# 1000steps = every 1ps
> dcdfreq 1000
> xstFreq 1000
> outputEnergies 10
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Minimization
> minimize 100
> reinitvels $temperature
>
> run 10000 ;# 10ps
>
> After running the simulation i have encountered the following error
>
> REINITIALIZING VELOCITIES AT STEP 100 TO 298 KELVIN.
> TCL: Running for 10000 steps
> ERROR: Atom 23573 velocity is -16230.5 -42310.9 16194.5 (limit is 12000)
> ERROR: Atoms moving too fast; simulation has become unstable.
> ERROR: Atom 11717 velocity is -26595 352.88 35945.3 (limit is 12000)
> ERROR: Atoms moving too fast; simulation has become unstable.
> ERROR: Atom 32740 velocity is 6234.49 -10573.8 3218.94 (limit is 12000)
> ERROR: Atoms moving too fast; simulation has become unstable.
> ERROR: Atom 10811 velocity is 20760.9 47547.2 -18996.4 (limit is 12000)
> ERROR: Atom 24548 velocity is 562.081 -1538.09 -21147.8 (limit is 12000)
> ERROR: Atoms moving too fast; simulation has become unstable.
> ERROR: Atom 23541 velocity is -5318.93 2372.28 14141.1 (limit is 12000)
> ERROR: Atom 25076 velocity is 19915.6 -32341.9 12263.8 (limit is 12000)
> ERROR: Atom 25838 velocity is 80549.7 -36561.9 -219838 (limit is 12000)
> ERROR: Atoms moving too fast; simulation has become unstable.
> ERROR: Atom 13300 velocity is 20625.6 13084.8 -2221.2 (limit is 12000)
> ERROR: Atoms moving too fast; simulation has become unstable.
> ERROR: Atom 11828 velocity is 82687.7 -32277.6 43229 (limit is 12000)
> ERROR: Atoms moving too fast; simulation has become unstable.
> ERROR: Atom 24167 velocity is -2496.97 7572.91 -10993.4 (limit is 12000)
> ERROR: Atoms moving too fast; simulation has become unstable.
> ERROR: Atom 33196 velocity is -913.896 21848.3 -7693.01 (limit is 12000)
> ERROR: Atoms moving too fast; simulation has become unstable.
> ERROR: Atom 12536 velocity is 18992.3 -35199.8 29699.8 (limit is 12000)
> ERROR: Atom 27931 velocity is 2720.71 7220.98 -10991.5 (limit is 12000)
> ERROR: Atoms moving too fast; simulation has become unstable.
> ERROR: Atom 9806 velocity is 63749.5 -334617 63478 (limit is 12000)
> ERROR: Atom 14958 velocity is -3915.41 21516.5 -4112.67 (limit is 12000)
> ERROR: Atom 24475 velocity is -17615.2 -6948.36 -35026.4 (limit is 12000)
> ERROR: Atoms moving too fast; simulation has become unstable.
> ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
>
> ENERGY: 100 89080.0711 15192.4248 2209.5977 216.1183 302922.0085 9999999999.9999 0.0000 0.0000 30021.9274 9999999999.9999 299.5870 9999999999.9999 9999999999.9999 299.5870 42540284.6972 7734007.8743 308102.3660 42540284.6972 7734007.8743
>
> ERROR: Exiting prematurely; see error messages above.
>
> Please help me to solve the problem
>
> Thanks
> --
> Prija Ponnan