From: Ranyere Deyler (ranyere_at_gmail.com)
Date: Sat May 08 2010 - 03:10:14 CDT
*Dear NAMD Users, i was trying to do an annealing in my system using a
script that i saw on the mail list. Basicaly i had the "langevin" turned on,
and in the end i tried to use the "reassignFreq" to heat up and then cool
down system. But i got this error: *
FINISHED WRITING RESTART VELOCITIES
REINITIALIZING VELOCITIES AT STEP 5000 TO 10 KELVIN.
TCL: Setting parameter reassignFreq to 2500
FATAL ERROR: Setting parameter reassignFreq from script failed!
FATAL ERROR: Setting parameter reassignFreq from script failed!
FATAL ERROR: Setting parameter reassignFreq from script failed!
FATAL ERROR: Setting parameter reassignFreq from script failed!
[3] Stack Traceback:
[0] CmiAbort+0x5f [0xabcdf3]
[1] _Z8NAMD_diePKc+0x62 [0x509172]
[2] _ZN13SimParameters9scriptSetEPKcS1_+0x548 [0x985e2a]
[3] _ZN4Node11scriptParamEP14ScriptParamMsg+0x1a [0x9112ac]
[4] _ZN12CkIndex_Node32_call_scriptParam_ScriptParamMsgEPvP4Node+0xf
[0x91128f]
[5] CkDeliverMessageFree+0x21 [0xa3414b]
[6] _Z15_processHandlerPvP11CkCoreState+0x530 [0xa3373c]
[7] CsdScheduleForever+0xa5 [0xabdbf1]
[8] CsdScheduler+0x1c [0xabd7f2]
[9] _Z11master_initiPPc+0x2d6 [0x512106]
[10] _ZN7BackEnd4initEiPPc+0x31 [0x511e29]
[11] main+0x2f [0x50d71f]
[12] __libc_start_main+0xf4 [0x7f28530c91c4]
[13] _ZNSt8ios_base4InitD1Ev+0x52 [0x508ada]
*I've seen just one case like this on the mail list, but had no solution.
One said to turn off the "lanvegin", but looking at the mail list i've seen
the "reassignFreq" beeing used together with the "langevin". Someone's got
any idea of what's wrong? Here's the conf file:*
##############################################################################
structure final.psf
coordinates final.pdb
set temperature 10
set outputname cnt_c60
firsttimestep 0
#############################################################
## SIMULATION PARAMETERS ##
#############################################################
# Input
paraTypeCharmm on
parameters par_nanotubes.inp
temperature $temperature
# Periodic Boundary conditions
cellBasisVector1 17.75 0. 0.
cellBasisVector2 0. 17.75 0.
cellBasisVector3 0. 0 84.90
wrapAll on
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 14.5
# Integrator Parameters
timestep 1 ;# 1fs/step
nonbondedFreq 2
fullElectFrequency 4
stepspercycle 20
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen no ;# don't couple langevin bath to hydrogens
# Output
outputName $outputname
restartfreq 5000 ;# 1000steps = every 1ps
dcdfreq 500
outputEnergies 500
# Fixed Atoms Constraint (set PDB occupancy-column to 1)
fixedAtoms on
#############################################################
## EXECUTION SCRIPT ##
#############################################################
# Minimization
minimize 5000
reinitvels $temperature
## Script pra fazer annealing!! (aquecer e resfriar)
reassignFreq 2500
reassignTemp 10
minimize 2500
for { set TEMP 10 } { $TEMP < 310 } { incr TEMP 10 } {
run 2500
reassignTemp $TEMP
}
run 2500
for { set TEMP 300 } { $TEMP > 0 } { incr TEMP -10 } {
reassignTemp $TEMP
run 2500
}
*
Thanks a lot.
Ranyere Deyler Trindade
*
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