Re: restarting heating protocol problem:

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue Sep 23 2008 - 14:29:49 CDT

Try "reassignTemp 0". NAMD calculates the temp based on the current
timestep, in this case 20000, and therefore assumes you want a temp
of 400 (199.937 + 20000*.01), and then sets it to 300.

On Sep 23, 2008, at 12:55 PM, Parminder Mankoo wrote:

> Hello,
>
> I am trying to run a restart of heating in NAMD. My first run
> stopped at 20,000 step with temp=199.937K. I used the following
> conf file for restart, by using bincoor and binvelocities.
> But the first output it prints in the log file is:
> "REASSIGNING VELOCITIES AT STEP 20000 TO 300 KELVIN
> ETITLE: TS BOND ANGLE
> DIHED IMPRP ELECT VDW
> BOUNDARY MISC KINETIC
> TOTAL TEMP TOTAL2 TOTAL3
> TEMPAVG PRESSURE GPRESSURE VOLUME
> PRESSAVG GPRESSAVG
>
> ENERGY: 20000 3121.5677 9762.5466 7318.4962
> 545.8575 -1214118.6359 144479.6058 1267.4101
> 0.0000 185224.4693 -862398.6828 300.1631
> -862296.7986 -862296.7986 300.1631
> 420.8836 496.8736 3278600.0000 420.8836 496.873"
> Shouldn't the first temp be 199.937K since that's what the vel and
> reassigntemp are telling it to be. It should start the same heating
> protocol from 199.937K to 300K instead of reassigning straight o
> 300K. Please let me know what I am doing wrong?
>
> Thanks,
> Parminder
> __________________________
> structure prot.psf
> Coordinates minicl30prot.coor
>
> bincoordinates heat2cl30prot.coor
> binvelocities heat2cl30prot.vel
>
> extendedSystem heat2cl30prot.xsc
>
> paraTypeXplor off
> paratypecharmm on
> parameters par_all22_prot.inp
> exclude scaled1-4
> 1-4scaling 1.0
>
> switching on
> switchdist 10
> cutoff 13
> pairlistdist 14
> margin 2.5
>
> PME on
> PMEGridSizeX 196 #EDIT THIS!
> PMEGridSizeY 128 #EDIT THIS!
> PMEGridSizeZ 128 #EDIT THIS!
>
> cellBasisVector1 194.0000 0 0 #EDIT THIS!
> cellBasisVector2 0 130.0000 0 #EDIT THIS!
> cellBasisVector3 0 0 130.0000 #EDIT THIS!
> cellOrigin 0.0 0.0 0.0 #EDIT THIS!
>
> # Integrator Parameters
> timestep 1.0
> rigidBonds all
> rigidTolerance 1.0e-6
> useSettle on
> nonbondedFreq 1
> fullElectFrequency 4
> stepspercycle 20
>
> wrapWater on
> #wrapAll on
>
>
> binaryoutput no
> restartname heat2-1cl30prot #EDIT THIS if you need!
> outputname heat2-1cl30prot #EDIT THIS! - your
> output filename
> restartfreq 1000 # 5000steps = every 7.5ps
> dcdfreq 1000
> xstFreq 1000
> outputEnergies 500
> outputPressure 500
> outputTiming 1000
>
> #temperature 199.9370
> seed 1010
>
> firsttimestep 20000
> numsteps 30000
>
> minimization off
>
> constraints on
> consref minicl30prot.coor
> conskfile prot-cl-30.pdb
> conskcol B
>
> reassignTemp 199.9370
> reassignFreq 1
> reassignIncr .01
> reassignHold 300
>
> numAtomsSelf 88
> numAtomsPair 140
>
> twoAwayX yes # when #atoms/#cpus < 200
> twoAwayY yes # when #atoms/#cpus < 50
> twoAwayZ yes # when #atoms/#cpus < 20

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