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标题: npt控压出现问题 [打印本页]

作者
Author: mol 时间: 2018-1-8 13:55
标题: npt控压出现问题
各位前辈，小弟目前在模拟原油体系在二氧化硅管内的输运现象，体系如下图：
(, 下载次数 Times of downloads: 28)

我想在z方向把油的密度压缩到平衡，使用mdp文件如下：
cpp                =  cpp
constraints       = all-bonds
constraint_algorithm =  LINCS
integrator       =  md
dt                =  0.0002 ; ps !
nsteps             =  10000000  ; 2 ns
nstxout          =  20000
nstvout          =  20000
nstfout          =  20000
nstlog             =  2000
nstenergy          =  20000
nstxtcout          =  20000
nstlist          =  10
ns_type          =  grid
coulombtype       =  PME
rlist             =  0.9
rcoulomb          =  0.9
rvdw             =  1.2
pbc                = xyz
optimize_fft       = yes
nstcomm          = 1
comm-grps          = system
; Berendsen temperature coupling is on
tcoupl             =  v-rescale
tc-grps          =  system
tau_t             =  0.1
ref_t             =  298
; Semiisotropic pressure coupling is now on
Pcoupl             =  Parrinello-Rahman;Berendsen
Pcoupltype       =  semiisotropic ; uniform scaling of x-y box vectors, independent z
tau_p             =  2.0             ; time constant, in ps
compressibility    =  0 4.5e-5       ; isothermal compressibility, bar^-1
ref_p             =  1.0 1.0       ; reference pressure, x-y, z (in bar)
; Energy monitoring
energygrps       =  system
;energygrp_excl    =  BOT BOT
; Generate velocites is on at 300K.
gen_vel          =  yes
gen_temp          =  298
gen_seed          =  173529
periodic_molecules  = yes

但是格子越来越大了呢，下面是g_energy输出的格子信息：

# This file was created Mon Jan  8 08:54:50 2018
# by the following command:
# g_energy -f npt.edr -s npt.tpr -o xyz.xvg
#
# g_energy is part of G R O M A C S:
#
# Grunge ROck MAChoS
#
@ title "Gromacs Energies"
@ xaxis  label "Time (ps)"
@ yaxis  label "(nm)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Box-X"
@ s1 legend "Box-Y"
@ s2 legend "Box-Z"
0.000000 9.820000 8.504370 35.447201
4.000000 9.820000 8.504370 33.942310
8.000000 9.820000 8.504370 33.552357
12.000000 9.820000 8.504370 33.600903
16.000000 9.820000 8.504370 34.145199
20.000000 9.820000 8.504370 34.654156
24.000000 9.820000 8.504370 34.983170
28.000000 9.820000 8.504370 35.425865
32.000000 9.820000 8.504370 36.125687
36.000000 9.820000 8.504370 36.763256
40.000000 9.820000 8.504370 37.417305
44.000000 9.820000 8.504370 38.256130
48.000000 9.820000 8.504370 39.084908
52.000000 9.820000 8.504370 39.968571
56.000000 9.820000 8.504370 40.995853
60.000000 9.820000 8.504370 41.994690
64.000000 9.820000 8.504370 43.178162
68.000000 9.820000 8.504370 44.334236
72.000000 9.820000 8.504370 45.668537
76.000000 9.820000 8.504370 47.013527
80.000000 9.820000 8.504370 48.472515
84.000000 9.820000 8.504370 50.007713
88.000000 9.820000 8.504370 51.560898
92.000000 9.820000 8.504370 53.230545
96.000000 9.820000 8.504370 54.987411
  100.000000 9.820000 8.504370 56.769543
  104.000000 9.820000 8.504370 58.653545
  108.000000 9.820000 8.504370 60.582832
  112.000000 9.820000 8.504370 62.578793
  116.000000 9.820000 8.504370 64.664238
  120.000000 9.820000 8.504370 66.800468
  124.000000 9.820000 8.504370 68.995361
  128.000000 9.820000 8.504370 71.256256
  132.000000 9.820000 8.504370 73.597328
  136.000000 9.820000 8.504370 75.975792
  140.000000 9.820000 8.504370 78.400414
  144.000000 9.820000 8.504370 80.899727
  148.000000 9.820000 8.504370 83.413765
  152.000000 9.820000 8.504370 85.927498
  156.000000 9.820000 8.504370 88.489822
  160.000000 9.820000 8.504370 91.083817
  164.000000 9.820000 8.504370 93.677811
  168.000000 9.820000 8.504370 96.271805
  172.000000 9.820000 8.504370 98.964058
  176.000000 9.820000 8.504370  101.710640
  180.000000 9.820000 8.504370  104.457222
  184.000000 9.820000 8.504370  107.203804
  188.000000 9.820000 8.504370  109.950386
  192.000000 9.820000 8.504370  112.807594
  196.000000 9.820000 8.504370  115.700119
  200.000000 9.820000 8.504370  118.599289
  204.000000 9.820000 8.504370  121.498459
  208.000000 9.820000 8.504370  124.397629
  212.000000 9.820000 8.504370  127.299461
  216.000000 9.820000 8.504370  130.351212
  220.000000 9.820000 8.504370  133.402969
  224.000000 9.820000 8.504370  136.454727
  228.000000 9.820000 8.504370  139.506485
  232.000000 9.820000 8.504370  142.558243
  236.000000 9.820000 8.504370  145.610001
  240.000000 9.820000 8.504370  148.661758
  244.000000 9.820000 8.504370  151.713516
  248.000000 9.820000 8.504370  154.765274
  252.000000 9.820000 8.504370  157.817032
  256.000000 9.820000 8.504370  160.868790
  260.000000 9.820000 8.504370  163.920547
  264.000000 9.820000 8.504370  167.238403
  268.000000 9.820000 8.504370  170.595337
  272.000000 9.820000 8.504370  173.952271
  276.000000 9.820000 8.504370  177.309204
  280.000000 9.820000 8.504370  180.666138
  284.000000 9.820000 8.504370  184.023071
  288.000000 9.820000 8.504370  187.380005
  292.000000 9.820000 8.504370  190.736938
  296.000000 9.820000 8.504370  194.093872
  300.000000 9.820000 8.504370  197.450806

请问各位大侠有可能是哪里出问题了？

作者
Author: sobereva 时间: 2018-1-8 18:20
既然步长都0.2fs了，all-bonds约束也没必要设了。先去了试试
乍看没有明显问题，但一些细节不好说。控压的设定反复再调节调节，再看看top文件有无毛病，反复试试

作者
Author: 虔诚的人 时间: 2018-4-26 17:36

sobereva 发表于 2018-1-8 18:20
既然步长都0.2fs了，all-bonds约束也没必要设了。先去了试试
乍看没有明显问题，但一些细节不好说。控压的 ...

sob老师，请问时间不长0.1fs和0.2fs是怎么选择的？为什么time steps=0.2 ps后就没必要设置all-bond了。

作者
Author: sobereva 时间: 2018-4-26 19:39

虔诚的人发表于 2018-4-26 17:36
sob老师，请问时间不长0.1fs和0.2fs是怎么选择的？为什么time steps=0.2 ps后就没必要设置all-bond了。{: ...

首先我并不建议用all-bonds约束，引入的人为因素不可忽略
对键进行约束，主要目的是为了消除高频振动，从而可以用更大的步长。0.2fs已经算是非常小了，这种情况下没有必要对键做任何约束。一般情况，<=1fs的步长都没必要做任何约束。

作者
Author: 虔诚的人 时间: 2018-4-27 19:53

sobereva 发表于 2018-4-26 19:39
首先我并不建议用all-bonds约束，引入的人为因素不可忽略
对键进行约束，主要目的是为了消除高频振动， ...

谢谢，sob老师，理解了

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