From: mj_aghaei_at_aut.ac.ir
Date: Wed Jul 25 2012 - 21:12:31 CDT
Hi everyone
I am trying to run a "tclBC" simulation, and NAMD hangs at "startup phase 8" (It does not parse "Info: Entering startup phase 8" in log file).
I have minimized the same model (without "tclBC") with no problem and my model runs smoothly with "tclForces" also.
The question is what is exactly done during "startup phase 8". Knowing that I may be able to figure out how to modify my model or configuration file to resolve the problem.
Thank you in advance
Regards
M. J. Aghaei
mj_aghaei_at_aut.ac.ir
P.S. Here is my configuration file if it helps;
structure SI_tube_wb.psf
coordinates SI_tube_wb.pdb
outputName SI_tube_wb_out
set temperature 298
firsttimestep 0
paraTypeCharmm on
parameters par_all27_prot_SI.inp
temperature $temperature
if {1} {
cellBasisVector1 77.415 0 0
cellBasisVector2 0 77.687 0
cellBasisVector3 0 0 209.178
cellOrigin -0.764 -1.115 20.092
}
wrapWater on
wrapAll on
exclude scaled1-4
1-4scaling 1.0
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 14.0
# Integrator Parameters
timestep 1 ;# 1fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 10
#PME
if {1} {
PME yes
PMEGridSpacing 1.0
}
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
restartfreq 500
dcdfreq 500
xstFreq 250
outputEnergies 100
outputPressure 100
if {0} {
tclForces on
tclForcesScript {
set force {0 0 0.1}
set watIdList {}
for {set i 4361} {$i<96427} {incr i 3} {
lappend watIdList $i
addatom $i
}
proc calcforces {} {
global watIdList force
loadcoords coorList
foreach i $watIdList {
set z [lindex $coorList($i) 2]
if {$z<-40 && $z>-70} {
addforce $i $force
}
}
}
}
}
if {1} {
tclBC on
tclBCScript {
wrapmode cell
proc calcforces {} {
while {[nextatom]} {
set rvec [getcoord]
set mass [getmass]
if { $mass<14 || $mass>17 } {
dropatom
}
foreach { x y z } $rvec { break }
if { $z<-40 && $z>-70 } {
addforce "0.0 0.0 0.1"
}
}
}
}
}
if {1} {
minimize 100
reinitvels $temperature
}
run 500000
And this is where it hangs;
Info: Startup phase 7 took 1.223 s, 90.8203 MB of memory in use
Info: CREATING 3662 COMPUTE OBJECTS
Info: useSync: 1 useProxySync: 0
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 2.64698e-023 AT 11.9138
Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 1.40436e-016 AT 11.9138
Info: ABSOLUTE IMPRECISION IN SCOR TABLE FORCE: 4.10282e-022 AT 11.9138
Info: RELATIVE IMPRECISION IN SCOR TABLE FORCE: 3.56912e-015 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWA TABLE ENERGY: 9.86076e-032 AT 11.8295
Info: RELATIVE IMPRECISION IN VDWA TABLE ENERGY: 6.75473e-014 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 4.62223e-032 AT 11.9138
Info: RELATIVE IMPRECISION IN VDWA TABLE FORCE: 2.12237e-015 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWB TABLE ENERGY: 4.1359e-025 AT 11.8295
Info: RELATIVE IMPRECISION IN VDWB TABLE ENERGY: 7.56853e-015 AT 11.9138
Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 3.87741e-026 AT 11.9138
Info: RELATIVE IMPRECISION IN VDWB TABLE FORCE: 5.97409e-016 AT 11.9138
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