Inquire on gradual temperature increase.

From: Diego Alejandro Vargas (vardiego9_at_gmail.com)
Date: Mon Oct 20 2008 - 08:59:46 CDT

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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