Re: Inquire on gradual temperature increase.

From: jose correa (corrjose_at_gmail.com)
Date: Mon Oct 20 2008 - 09:39:40 CDT

Dear Diego
I do not sure, but, I think that you need to block the minimization by
adding # previously to minimize 2000.
Best wishes
J Correa-Basusto
ESM-IPN,Mexico

2008/10/20 Diego Alejandro Vargas <vardiego9_at_gmail.com>:
> Hi,
> I am trying to run a minimization and equilibration simulation on fascin.
> After minimization once run starts I am getting the following error message:
>
> ENERGY: 2000 7742052.1757 999944.6299 11650.2374
> 26481.1536
> -688125.1118 99999999.9999 0.0000 0.0000
> 0.0000
> 99999999.9999 0.0000 99999999.9999 99999999.9999
> 0.0000
> 99999999.9999 99999999.9999 128064.0000 99999999.9999 99999999.9999
>
> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 2000
> WRITING COORDINATES TO DCD FILE AT STEP 2000
> WRITING COORDINATES TO RESTART FILE AT STEP 2000
> FINISHED WRITING RESTART COORDINATES
> WRITING VELOCITIES TO RESTART FILE AT STEP 2000
> FINISHED WRITING RESTART VELOCITIES
> REINITIALIZING VELOCITIES AT STEP 2000 TO 310 KELVIN.
> TCL: Running for 250000 steps
> ERROR: Constraint failure in RATTLE algorithm for atom 5690!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Constraint failure in RATTLE algorithm for atom 3906!
> ERROR: Constraint failure in RATTLE algorithm for atom 4304!
> ERROR: Constraint failure in RATTLE algorithm for atom 67!
> ERROR: Constraint failure in RATTLE algorithm for atom 5491!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Constraint failure in RATTLE algorithm for atom 2834!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Constraint failure in RATTLE algorithm for atom 1907!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Constraint failure in RATTLE algorithm for atom 156!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Constraint failure in RATTLE algorithm for atom 133!
> ERROR: Constraint failure; simulation has become unstable.
> ERROR: Exiting prematurely.
> _________________________________
>
> From the mailing list archive and a previous posting I believe the problem
> lies in reinitializing velocities at 310K immediately instead of using a
> gradual decrease. My question is, what is the best way to do this?
>
> + At what temperature should the system start? I have seen both 0K or just
> double digit temperatures used.
> + I considered using the following code:
>
> reassignFreq 500
> reassignTemp 0
> reassignIncr 10
> reassignHold 310
>
> But I don't know how this would conflict with the langevinTemp defined
> previously in the configuration file?
>
> + Another option is a for loop reassigning a new value to langevinTemp:
>
> run 500
> for {set i 0} {$i <= 310} {incr i 10} {
> langevinTemp $i
> run 500
> }
>
> But again, where to put this within configuration file? Instead if
> reinitvels before run? Would it then be necessary to turn off langevinPiston
> and turn it on again after this loop? I am including my configuration file
> at the bottom in case anybody wants to see it.
>
> Thank you for your attention,
> Diego A. Vargas
> ___________________________________________________
>
> structure ***
> coordinates ***
>
>
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
>
> structure ***
> coordinates ***
>
> set temperature 310
> set outputname ***
>
> firsttimestep 0
>
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters ../common/par_all27_prot_lipid.inp
> temperature $temperature
>
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 10.
> pairlistdist 13.5
>
>
> # Integrator Parameters
> timestep 2.0 ;# 2fs/step
> rigidBonds all
> 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 48. 0. 0.
> cellBasisVector2 0. 58. 0.
> cellBasisVector3 0. 0 46.
> cellOrigin 62. 89. 10.
>
> wrapAll on
>
>
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 50
> PMEGridSizeY 50
> PMEGridSizeZ 50
>
>
> # Constant Pressure Control (variable volume)
> useGroupPressure yes ;# needed for rigidBonds
> useFlexibleCell no
> useConstantArea no
>
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 100.
> langevinPistonDecay 50.
> langevinPistonTemp $temperature
>
>
> # Output
> outputName $outputname
>
> restartfreq 500 ;# 500steps = every 1ps
> dcdfreq 250
> xstFreq 250
> outputEnergies 100
> outputPressure 100
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Minimization
> minimize 2000
> reinitvels $temperature
>
> run 250000 ;# 500ps
>
>

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