计算化学公社

标题: 用VASP模拟32个水分子，结果氢氧键断裂了 [打印本页]

作者
Author: ra2ghgzh 时间: 2017-4-25 21:48
标题: 用VASP模拟32个水分子，结果氢氧键断裂了
INCAR如下：
System=H2O
ISTART=0
ICHARG=2
LCHARG=.F.
LWAVE=.F.
PREC=High

LREAL=A
NELM=60
ISMEAR=-1
SIGMA=0.05
NELMIN=10

EDIFF=1E-05
IBRION=0
IALGO=48
NSW=10
POTIM=1
ISIF=2
NBLOCK=1
KBLOCK=50
APACO=10
NPACO=200
TEBEG=300
TEEND=300
SMASS=-3

结果发现有的氧原子上一个氢都不连，直接崩溃

作者
Author: jiangning198511 时间: 2017-4-26 09:00
你把最后的结构贴出了看看，估计是周期性边界条件显示的问题

作者
Author: ra2ghgzh 时间: 2017-4-26 09:09

jiangning198511 发表于 2017-4-26 09:00
你把最后的结构贴出了看看，估计是周期性边界条件显示的问题

New structure
1.00000000000000
   9.7388696670999995 0.0000000000000000 0.0000000000000000
   0.0000000000000000 9.7388696670999995 0.0000000000000000
   0.0000000000000000 0.0000000000000000 9.7388696670999995
H O
64 32
Direct
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作者
Author: ra2ghgzh 时间: 2017-4-26 09:11

jiangning198511 发表于 2017-4-26 09:00
你把最后的结构贴出了看看，估计是周期性边界条件显示的问题

我是想用这种方法做显式溶剂的计算，如果这条路走不通的话就得学Gromacs了。

作者
Author: jiangning198511 时间: 2017-4-26 10:04

ra2ghgzh 发表于 2017-4-26 09:11
我是想用这种方法做显式溶剂的计算，如果这条路走不通的话就得学Gromacs了。

结构确实有些键断了，感觉挺奇怪的，是否是模拟时间太短了，以及初始结构有错误？，第一性原理处理水溶剂的计算结果有报道，用VASP的文章也有很多

作者
Author: ra2ghgzh 时间: 2017-4-26 10:28

jiangning198511 发表于 2017-4-26 10:04
结构确实有些键断了，感觉挺奇怪的，是否是模拟时间太短了，以及初始结构有错误？，第一性原理处理水溶剂 ...

我把输入文件和CONTCAR放到附件中了，麻烦您给看看，谢谢。

(, 下载次数 Times of downloads: 19)

作者
Author: jiangning198511 时间: 2017-4-26 12:09

ra2ghgzh 发表于 2017-4-26 10:28
我把输入文件和CONTCAR放到附件中了，麻烦您给看看，谢谢。

你这个坐标文件(POSCAR）有问题，好像是CONTCAR, 并且POSCAR 里面的键已经断了，你再检查一下

作者
Author: ra2ghgzh 时间: 2017-4-26 13:44

jiangning198511 发表于 2017-4-26 12:09
你这个坐标文件(POSCAR）有问题，好像是CONTCAR, 并且POSCAR 里面的键已经断了，你再检查一下

嗯，我弄错了POSCAR应该是：
New structure
1.0
      9.7388696671       0.0000000000       0.0000000000
      0.0000000000       9.7388696671       0.0000000000
      0.0000000000       0.0000000000       9.7388696671
H O
64 32
Direct
   0.608640015       0.790790021       0.396479994
   0.477169991       0.883700013       0.396479994
   0.501770020       0.643130004       0.388819993
   0.370290011       0.736060023       0.388819993
   0.618130028       0.807079971       0.229939997
   0.486649990       0.899999976       0.229939997
   0.511250019       0.659430027       0.222289994
   0.379779994       0.752349973       0.222289994
   0.852400005       0.621980011       0.249300003
   0.720910013       0.714900017       0.249300003
   0.745519996       0.474319994       0.241650000
   0.614030004       0.567250013       0.241650000
   0.856999993       0.608969986       0.397249997
   0.725520015       0.701889992       0.397249997
   0.751349986       0.463070005       0.387870014
   0.619859993       0.555989981       0.387870014
   0.594389975       0.758690000       0.729560018
   0.462920010       0.851610005       0.729560018
   0.487520009       0.611029983       0.721910000
   0.356040001       0.703949988       0.721910000
   0.603879988       0.774990022       0.563019991
   0.472400010       0.867900014       0.563019991
   0.497009993       0.627330005       0.555369973
   0.365520000       0.720250010       0.555369973
   0.838140011       0.589879990       0.582379997
   0.706659973       0.682799995       0.582379997
   0.731260002       0.442229986       0.574729979
   0.599789977       0.535139978       0.574729979
   0.842760026       0.576860011       0.730329990
   0.711269975       0.669790030       0.730329990
   0.737100005       0.430960000       0.720950007
   0.605610013       0.523890018       0.720950007
   0.395610005       0.459820002       0.443850011
   0.264129996       0.552739978       0.443850011
   0.288729995       0.312169999       0.436199993
   0.157240003       0.405090004       0.436199993
   0.405090004       0.476110011       0.277319998
   0.273609996       0.569040000       0.277319998
   0.298220009       0.328460008       0.269659996
   0.166730002       0.421380013       0.269659996
   0.639349997       0.291009992       0.296680003
   0.507879972       0.383929998       0.296680003
   0.532469988       0.143360004       0.289029986
   0.400999993       0.236279994       0.289029986
   0.643959999       0.277999997       0.444629997
   0.512480021       0.370920002       0.444629997
   0.538309991       0.132100001       0.435240000
   0.406819999       0.225009993       0.435240000
   0.381359994       0.427720010       0.776929975
   0.249870002       0.520630002       0.776929975
   0.274479985       0.280059993       0.769280016
   0.143000007       0.372990012       0.769280016
   0.390839994       0.444009990       0.610400021
   0.259359986       0.536930025       0.610400021
   0.283960015       0.296359986       0.602750003
   0.152480006       0.389270008       0.602750003
   0.625100017       0.258910000       0.629750013
   0.493629992       0.351830006       0.629750013
   0.518230021       0.111249998       0.622099996
   0.386750013       0.204170004       0.622099996
   0.629710019       0.245900005       0.777710021
   0.498230010       0.338820010       0.777710021
   0.524049997       0.100000001       0.768320024
   0.392580003       0.192919999       0.768320024
   0.510070026       0.790790021       0.396479994
   0.403200001       0.643130004       0.388819993
   0.519559979       0.807079971       0.229939997
   0.412669986       0.659430027       0.222289994
   0.753820002       0.621980011       0.249300003
   0.646939993       0.474319994       0.241650000
   0.758419991       0.608969986       0.397249997
   0.652769983       0.463070005       0.387870014
   0.495819986       0.758690000       0.729560018
   0.388949990       0.611029983       0.721910000
   0.505299985       0.774990022       0.563019991
   0.398429990       0.627330005       0.555369973
   0.739570022       0.589879990       0.582379997
   0.632690012       0.442229986       0.574729979
   0.744180024       0.576860011       0.730329990
   0.638520002       0.430960000       0.720950007
   0.297039986       0.459820002       0.443850011
   0.190149993       0.312169999       0.436199993
   0.306510001       0.476110011       0.277319998
   0.199640006       0.328460008       0.269659996
   0.540780008       0.291009992       0.296680003
   0.433899999       0.143360004       0.289029986
   0.545390010       0.277999997       0.444629997
   0.439729989       0.132100001       0.435240000
   0.282779992       0.427720010       0.776929975
   0.175899997       0.280059993       0.769280016
   0.292270005       0.444009990       0.610400021
   0.185389996       0.296359986       0.602750003
   0.526530027       0.258910000       0.629750013
   0.419660002       0.111249998       0.622099996
   0.531140029       0.245900005       0.777710021
   0.425480008       0.100000001       0.768320024

作者
Author: jiangning198511 时间: 2017-4-26 13:56

ra2ghgzh 发表于 2017-4-26 13:44
嗯，我弄错了POSCAR应该是：
New structure
1.0

你这个初始结构很奇怪，你能否用软件随机产生32水的结构，还有，你可以先做个几何结构优化，然后再试试AIMD,

作者
Author: ra2ghgzh 时间: 2017-4-26 20:18

jiangning198511 发表于 2017-4-26 13:56
你这个初始结构很奇怪，你能否用软件随机产生32水的结构，还有，你可以先做个几何结构优化，然后再试试AI ...

嗯，我刚才用anonymous cell生成了34个水，然后用forcite做了优化，目前为止还没跑散。
多谢二位。

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