Re: restarting heating protocol problem:

From: Parminder Mankoo (pmankoo1_at_jhu.edu)
Date: Tue Sep 23 2008 - 14:37:32 CDT

Thank you.

Instead I tried setting "firsttimestep =0" and "numsteps = 10K", and now it seems to be have the correct temp which makes sense based on your formula for temp.

"ENERGY: 0 3121.5677 9762.5466 7318.4962 545.8575 -1214118.6359 144479.6058 1267.4101 0.0000 123482.9790 -924140.1730 200.1087 -924043.0641 -924043.0641 200.1087 -23.2090 52.1603 3278600.0000 -23.2090 52.1603"

Best,
Parminder

----- Original Message -----
From: JC Gumbart <gumbart_at_ks.uiuc.edu>
Date: Tuesday, September 23, 2008 3:29 pm
Subject: Re: namd-l: restarting heating protocol problem:
To: Parminder Mankoo <pmankoo1_at_jhu.edu>
Cc: namd-l_at_ks.uiuc.edu

> 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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