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标题: 求助：1个NH4HSO4和200H2O的混合物模拟出现的问题 [打印本页]

作者
Author: chendpldxy 时间: 2017-5-10 12:47
标题: 求助：1个NH4HSO4和200H2O的混合物模拟出现的问题
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

作者
Author: sobereva 时间: 2017-5-10 13:23
mdp倒没什么问题
要么是拓扑文件的事（可以模拟个单独的NH4HSO4）看看结构是否合理，要么是初始结构的事，比如堆得太密，有不合理接触，能量极小化又没做太充分等。
如果确定上述细节都无误，把dt改为0.001，跑100ps，等体系充分弛豫开之后再换成0.002

作者
Author: chendpldxy 时间: 2017-5-10 13:56
谢谢 sobereva老师

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