Re: Temperature reassignment

From: Thomas Evangelidis (tevang3_at_gmail.com)
Date: Wed Jan 01 2014 - 09:27:57 CST

Energy minimization is like dropping the temperature of the system to 0
Kelvin. Therefore, in order to initialize velocities at 303 Kelvin you must
first do the gradual heating from 0->303 K otherwise the system will blow
up. Unlike GROMACS or AMBER, NAMD does not do the heating automatically.
Replace "run 1000000" with something like:

    # Heating
    set HeatSteps 5
    set HeatMDsteps 1000
    for {set i 1} {$i <= $HeatSteps } { incr i } {
        set t [expr $temp*$i/$HeatSteps]; puts "Heat structure to $t K for
$HeatMDsteps steps."
        reinitvels $t
        run $HeatMDsteps
    }
    reinitvels $temp
    run 1000000 ;# 1 ns at $temp Kelvin

Also are you sure you want to use a timestep of 1 fs?

On 31 December 2013 19:28, PANAGIOTA KYRIAKOU <kyria008_at_gmail.com> wrote:

> Hello,
>
> I have been trying to equilibrate my system that consists of protein
> embedded in a membrane and I get the following error:
>
> *TIMING: 500000 CPU: 9750.65, 0.021551/step Wall: 9750.65,
> 0.021551/step, 0 hours remaining, 556.101562 MB of memory in use.*
> *ETITLE: TS BOND ANGLE DIHED
> IMPRP ELECT VDW BOUNDARY
> MISC KINETIC TOTAL TEMP
> POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE
> VOLUME PRESSAVG GPRESSAVG*
> *ENERGY: 500000 48376.8664 114689
> <8664%20%C2%A0%20%C2%A0114689>.7899 11643.7243 506.4399
> -580965.4098 103191 <4098%20%C2%A0%20%C2%A0103191>.7767 0.0000
> 246.2954 0.0000 -302310.5171 0.0000
> -302310.5171 -302310.5171 0.0000 6488.4885
> 6928.4046 1914140.8650 6488.4885 6928.4046*
>
> *WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 500000*
> *WRITING COORDINATES TO DCD FILE AT STEP 500000*
> *WRITING COORDINATES TO RESTART FILE AT STEP 500000*
> *FINISHED WRITING RESTART COORDINATES*
> *WRITING VELOCITIES TO RESTART FILE AT STEP 500000*
> *FINISHED WRITING RESTART VELOCITIES*
> *TCL: Writing to files with basename A_equil_1_min.*
> *WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 500000*
> *WRITING COORDINATES TO OUTPUT FILE AT STEP 500000*
> *WRITING VELOCITIES TO OUTPUT FILE AT STEP 500000*
> *TCL: Running for 1000000 steps*
> *REASSIGNING VELOCITIES AT STEP 500000 TO 303.15 KELVIN.*
> *colvars: Writing the state file "A_equil_1.restart.colvars.state".*
> *colvars: Synchronizing (emptying the buffer of) trajectory file
> "A_equil_1.colvars.traj".*
> *ERROR: Constraint failure in RATTLE algorithm for atom 6522!*
> *ERROR: Constraint failure; simulation has become unstable.*
> *ERROR: Constraint failure in RATTLE algorithm for atom 13834!*
> *ERROR: Constraint failure; simulation has become unstable.*
> *ERROR: Constraint failure in RATTLE algorithm for atom 1812!*
> *ERROR: Constraint failure; simulation has become unstable.*
>
> When I tried to fix it I realized that the Temperature increased from 0 to
> 312 K, instantly after minimization even though I am using temperature
> reassignment. Here is my configuration file:
>
>
> *#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#*
> *# Custom variables*
> *set temp 303.15 *
>
> *# inputs*
> * structure ../A.psf ; *
> * coordinates ../A.pdb ;*
> * paraTypeCharmm on*
> * parameters ../../common/topology/par_all36_prot_nomass.prm*
> * parameters ../../common/topology/par_all36_water_ions.prm *
> * parameters ../../common/topology/par_all36_lipid.prm *
>
>
> * temperature $temp ;*
> * # simulation parameters*
> * outputname A_equil_1 ;*
> * outputEnergies 1000 ;*
> * outputTiming 1000 ;*
> * xstFreq 10000 ;*
> * dcdFreq 10000 ;*
> * dcdUnitCell yes *
> * binaryoutput on ;*
> * restartfreq 10000 ;*
> * seed 1369948321 ;*
>
> *# calculation parameters*
> * exclude scaled1-4 ;*
> * 1-4scaling 1.0 ;*
> * switching on ;*
> * switchDist 9 ;*
> * cutoff 10 ;*
> * pairlistdist 12 ; *
> * stepsPerCycle 20 ;*
> * rigidbonds all ;*
> * vdwForceSwitching yes ;*
> * timestep 1 ; *
> * nonBondedFreq 1 ;*
> * fullElectFrequency 1 ;*
> * cellBasisVector1 139.65999603271484 00.00 00.00 ;*
> * cellBasisVector2 00.00 140.35699462890625 00.00 ;*
> * cellBasisVector3 00.00 00.00 97.64900207519531 ;*
> * cellorigin -0.9953396916389465 4.457383155822754
> 2.071026086807251 ;*
> * wrapAll on ;*
> * wrapWater on ;*
> * wrapNearest off ;*
>
> *# PME*
> * Pme on ;*
> * PmeGridsizeX 144 ;*
> * PmeGridsizeY 150 ;*
> * PmeGridsizeZ 108 ;*
>
>
> *# Control (need to be specified before runs) *
> * useFlexibleCell yes ;*
> * useGroupPressure yes ;*
> * useConstantRatio yes ;*
>
> *# constant pressure*
> * langevinPiston on*
> * langevinPistonTarget 1.01325*
> * langevinPistonPeriod 50.0*
> * langevinPistonDecay 25.0*
> * langevinPistonTemp $temp*
>
> * reassignFreq 1000 ;*
> * reassignTemp 1 ;*
> * reassignIncr 1 ;*
> * reassignHold $temp ; *
>
> * colvars on*
> * colvarsConfig ../restraints/A_equil_1.col *
>
>
> *#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#*
> * # EXECUTION*
>
> *#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#*
> * minimize 500000*
>
> * run 1000000*
>
>
> Do you know what could have caused the increase in the temperature?
> I would appreciate your help so much,
>
> Giota
>
> Panagiota Kyriakou
>
> Graduate Student
>
> Dept. of Chemical Engineering and Materials Science
>
> University of Minnesota
>
>
> email: kyria008_at_umn.edu
>

-- 
======================================================================
Thomas Evangelidis
PhD student
University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
Panepistimioupoli-Zografou
157 71 Athens
GREECE
email: tevang_at_pharm.uoa.gr
          tevang3_at_gmail.com
website: https://sites.google.com/site/thomasevangelidishomepage/

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