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各位大侠,我用Packmol生成200个水分子15HSO4-离子,1NH4+离子的混合物,box为[60A*60A*60A], 电荷用的是RESP电荷,结果一跑就出错,单独水滴的我试了下,没有问题,报错如下:不知啥原因?
md.mdp文件如下:
define =
integrator = md
dt = 0.002 ; ps
nsteps = 150000 ; 300ps
comm-grps = system
energygrps =
;
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 500
nstenergy = 500
nstxout-compressed = 1000
compressed-x-grps = system
;
annealing = single
annealing_npoints = 2
annealing_time = 0 50 ;ps
annealing_temp = 0 298.15
;
pbc = xyz
cutoff-scheme = group
nstlist = 1
rlist = 0.9
coulombtype = cut-off
rcoulomb = 0.9
vdwtype = cut-off
rvdw = 0.9
DispCorr = no
;
Tcoupl = V-rescale
tau_t = 0.2
tc_grps = system
ref_t = 298.15
;
gen_vel = no
gen_temp = 298.15
gen_seed = -1
;
freezegrps =
freezedim =
constraints = hbonds
出错信息如下:
Step 159, time 0.318 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000000, max 0.000000 (between atoms 610 and 609)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
610 609 77.2 0.3071 0.0973 0.0973
610 609 77.2 0.3071 0.0973 0.0973
610 609 77.2 0.3071 0.0973 0.0973
610 609 77.2 0.3071 0.0973 0.0973
610 609 77.2 0.3071 0.0973 0.0973
610 609 77.2 0.3071 0.0973 0.0973
610 609 77.2 0.3071 0.0973 0.0973
610 609 77.2 0.3071 0.0973 0.0973
Step 160, time 0.32 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 2.216318, max 2.216318 (between atoms 610 and 609)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
610 609 90.0 0.0973 0.3129 0.0973
610 609 90.0 0.0973 0.3129 0.0973
610 609 90.0 0.0973 0.3129 0.0973
610 609 90.0 0.0973 0.3129 0.0973
610 609 90.0 0.0973 0.3129 0.0973
610 609 90.0 0.0973 0.3129 0.0973
610 609 90.0 0.0973 0.3129 0.0973
610 609 90.0 0.0973 0.3129 0.0973
Wrote pdb files with previous and current coordinates
Step 161, time 0.322 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000003, max 0.000003 (between atoms 610 and 609)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
610 609 79.4 0.3129 0.0973 0.0973
610 609 79.4 0.3129 0.0973 0.0973
610 609 79.4 0.3129 0.0973 0.0973
610 609 79.4 0.3129 0.0973 0.0973
610 609 79.4 0.3129 0.0973 0.0973
610 609 79.4 0.3129 0.0973 0.0973
610 609 79.4 0.3129 0.0973 0.0973
610 609 79.4 0.3129 0.0973 0.0973
-------------------------------------------------------
Program: gmx mdrun, version 2016.1
Source file: src/gromacs/mdlib/constr.cpp (line 167)
MPI rank: 2 (out of 4)
Fatal error:
Too many LINCS warnings (1000)
If you know what you are doing you can adjust the lincs warning threshold in
your mdp file
or set the environment variable GMX_MAXCONSTRWARN to -1,
but normally it is better to fix the problem
For more information and tips for troubleshooting, please check the GROMACS
求各位大侠帮我看看
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