Re: Restart Simulation

From: Brian Bennion (bennion1_at_llnl.gov)
Date: Tue Jan 16 2007 - 10:42:45 CST

Hello Karol,
Look for posts with keywords gradual heating.
Its not the best thing in the world to shock your system with 310K
worth of energy and expect rattle to compensate.

Regards
Brian
At 03:49 AM 1/16/2007, Karol Kaszuba wrote:

> Dear NAMD users,
>
>I have a problem with restarting the simulation. I read all messages about it
>in NAMD mailing list but I didn't find a solution.
>
>1. I initailly minimized my complex and run MD (50000 steps = 100ps) with
>totally fixed protein.
>
>2. I want to restart a simulation but without initiall energy minimization. At
>the beginning of the run I obtained an error (see a message attached below)
>which informs that I have some bad water - protein contacts - generally it is
>possible but:
>this same error - (realted to THESE SAME atoms) I obtained when I tried to run
>my first equilibration phase (point 1) without E.min. It seems that NAMD
>ignores previously generated: restart coordinates, velocities and cell
>parameters and takes "standard" psf and pdb as the inputs.
>I have been trying a various combinations of configure file (see a conf. file
>below the error message)- still nothing.
>
> Any help will be appreciable.
>
>Yours sincerely,
>
>Karol
>
>
>Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 4.3715e-16 AT 0.03125
>Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 1.00929e-16 AT 0.231756
>Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 3.70577e-22 AT 11.9974
>Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 2.80873e-16 AT 11.9138
>Info: ABSOLUTE IMPRECISION IN SCOR TABLE ENERGY: 2.91168e-22 AT 11.9974
>Info: RELATIVE IMPRECISION IN SCOR TABLE ENERGY: 6.16001e-17 AT 11.9974
>Info: ABSOLUTE IMPRECISION IN SCOR TABLE FORCE: 1.98523e-22 AT 11.9974
>Info: RELATIVE IMPRECISION IN SCOR TABLE FORCE: 8.0593e-16 AT 11.9138
>Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 1.97215e-31 AT 11.8295
>Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 6.72641e-14 AT 11.9138
>Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 8.32002e-32 AT 11.9974
>Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 1.83939e-15 AT 11.9138
>Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 8.80495e-26 AT 11.9974
>Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 7.56853e-15 AT 11.9138
>Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 5.16988e-26 AT 11.9138
>Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 7.96546e-16 AT 11.9138
>Info: Entering startup phase 8 with 22320 kB of memory in use.
>Info: Finished startup with 25908 kB of memory in use.
>TCL: Running for 100000 steps
>ERROR: Constraint failure in RATTLE algorithm for atom 1620!
>ERROR: Constraint failure; simulation has become unstable.
>ERROR: Exiting prematurely.
>
>
>RESTART CONFIGURATION FILE:
>
>
>structure structureX_wb_ion.psf
>coordinates structureX_wb_ion.pdb
>
>set temperature 310
>set outputname structureX_wb_ion_all_system_moves
>outputname $outputname
>
>
># Continuing a job from the restart files
>
>if {1} {
>set inputname structureX_fixed.restart
>binCoordinates $inputname.coor
>binVelocities $inputname.vel
>extendedSystem $inputname.xsc
>}
>firsttimestep 0
>
>
>
># Input
>paraTypeCharmm on
>parameters par_all22_prot.inp
>
># Force-Field Parameters
>exclude scaled1-4
>1-4scaling 1.0
>cutoff 12.
>switching on
>switchdist 10.
>pairlistdist 13.5
>
># Integrator Parameters
>timestep 2.0
>rigidBonds all
>nonbondedFreq 1
>fullElectFrequency 2
>stepspercycle 10
>
># Constant Temperature Control
>langevin on
>langevinDamping 5
>langevinTemp $temperature
>langevinHydrogen no
>
>
>wrapWater on
>wrapAll on
>
>
>
>#PME
>
>PME yes
>PMEGridSizeX 80
>PMEGridSizeY 84
>PMEGridSizeZ 84
>
>
>
>
># Constant Pressure Control
>
>useGroupPressure yes
>useFlexibleCell no
>useConstantArea no
>
>langevinPiston on
>langevinPistonTarget 1.01325 ;# in bar -> 1 atm
>langevinPistonPeriod 100.
>langevinPistonDecay 50.
>langevinPistonTemp $temperature
>
>margin 2.5
>
>
>restartfreq 10000 ;# 10000steps = every 20ps
>dcdfreq 250 ;# = 400 x dcd
>xstFreq 250
>outputEnergies 100
>outputPressure 100
>
>
>
>
># Fixed Atoms Constraint (set PDB beta-column to 1)
>
>fixedAtoms on
>fixedAtomsFile structureX_cys94-cys144_fixed.pdb
>fixedAtomsCol B
>
>
>
>#############################################################
>## EXECUTION SCRIPT ##
>#############################################################
>
>
>run 100000 ;# 200ps

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