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大家好， 很高兴加入此论坛认识大家。最近我在学习NAMD2.9 source code (因为要使用 Plumed2.1.2，NAMD可匹配的最高版本也就NAMD2.9了)。在安装二者后，我做教程测试，均成功。但当我测试自己体系（蛋白-配体复合物，amber 99sb立场）时却始终显示一下多条类似错误：
ERROR: Constraint failure in RATTLE algorithm for atom 107!
ERROR: Constraint failure; simulation has become unstable.
事实上，这个体系之前使用NAMD_2.11_Linux-x86_64-multicore-CUDA是OK的，用别人家的NAMD2.9 source code测试也是OK的。以下是我的配置文件：
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
google给出的大部分建议是在最小化，加热和平衡过程，分步限制、放松最小化。我尝试多次，而且还更换多个体系，但仍是此类错误。所以很困惑，不知道大家遇到过这样问题没，希望得到指点。谢谢关注和留言。
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发表于 Post on 2017-8-26 13:31:15
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