From: 王茜茜 (wangqq430_at_gmail.com)
Date: Fri Aug 25 2017 - 22:47:16 CDT
Dear developer,
Recently, I need to use NAMD2.9 source code (because I want to learn
Plumed2.1.2). After installing both two softwares, I tested the given
examples in the manual and both worked well.
Then, I tested my system that worked well previously with
NAMD_2.11_Linux-x86_64-multicore-CUDA. However, when using NAMD2.9 source
code, it always gave the error:
ERROR: Constraint failure in RATTLE algorithm for atom 107!
ERROR: Constraint failure; simulation has become unstable.
The following is my conf:
amber yes
parmfile com_sol.prmtop
ambercoor com_sol.inpcrd
set temperature 310
set outputname ../output/md
# Continuing a job from the restart files
if {1} {
set inputname eq3
binCoordinates ../output/$inputname.restart.coor
binVelocities ../output/$inputname.restart.vel ;# remove the
"temperature" entry if you use this!
extendedSystem ../output/$inputname.restart.xsc
}
exclude scaled1-4
1-4scaling 0.833333
cutoff 12.0
switching off
switchdist 10.0
pairlistdist 13.5
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 20
rigidTolerance 0.00001
# 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
# Periodic Boundary Conditions
wrapAll on
# PME (for full-system periodic electrostatics)
PME yes
PMEGridSizeX 72
PMEGridSizeY 72
PMEGridSizeZ 80
# Constant Pressure Control (variable volume)
if {1} {
useGroupPressure yes ;# needed for 2fs steps
useFlexibleCell no ;# no for water box, yes for membrane
useConstantArea no ;# no for water box, yes for membrane
langevinPiston on
langevinPistonTarget 1.01325 ;# in bar -> 1 atm
langevinPistonPeriod 200.0
langevinPistonDecay 100.0
langevinPistonTemp $temperature
}
# Output
outputName $outputname
restartfreq 1000 ;# 500steps = every 1ps
dcdfreq 1000
xstFreq 1000
run 25000
I have minimized the system for many times and tried other systems, and
obtained same error. Actually, my system worked well in other machines with
NAMD2.9 source code. So, I donot know why. It confused me for two weeks.
so, dear developer, may you give me a help?
Qianqian
Macao university
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