| 查看: 4454 | 回复: 7 | ||
liuchenhan新虫 (小有名气)
|
[求助]
DNA模拟 已有1人参与
|
|
本人最近做DNA的模拟，遇到如下问题，刚开始做，很多东西还不懂，希望大神指点一下。脚本文件与数据文件上传了。 LAMMPS (14 May 2013) Scanning data file ... 3 = max bonds/atom 6 = max angles/atom 14 = max dihedrals/atom 1 = max impropers/atom Reading data file ... orthogonal box = (-10.907 -10.699 -2.821) to (9.961 16.557 134.259) 1 by 1 by 1 MPI processor grid 2640 atoms 2839 bonds 5116 angles 8346 dihedrals 200 impropers Finding 1-2 1-3 1-4 neighbors ... 4 = max # of 1-2 neighbors 7 = max # of 1-3 neighbors 18 = max # of 1-4 neighbors 20 = max # of special neighbors Finding SHAKE clusters ... 560 = # of size 2 clusters 120 = # of size 3 clusters 40 = # of size 4 clusters 0 = # of frozen angles PPPM initialization ... WARNING: System is not charge neutral, net charge = -80 (../pppm.cpp:267) G vector (1/distance)= 0.250095 grid = 12 15 45 stencil order = 5 estimated absolute RMS force accuracy = 0.0239292 estimated relative force accuracy = 7.20622e-05 using double precision FFTs 3d grid and FFT values/proc = 20900 8100 Setting up run ... WARNING: Inconsistent image flags (../domain.cpp:594) WARNING: Bond/angle/dihedral extent > half of periodic box length (../domain.cpp:667) Memory usage per processor = 15.2446 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = 3810376070790533.0000 KinEng = 0.0000 Temp = 0.0000 PotEng = 3810376070790533.0000 E_bond = 46241.5899 E_angle = 8875.0528 E_dihed = 2838.1521 E_impro = 0.0019 E_vdwl = 3810376070730726.0000 E_coul = 29596.0619 E_long = -27743.5161 Press = 13404015013180646.0000 ERROR on proc 0: Out of range atoms - cannot compute PPPM (../pppm.cpp:1888) -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. |
回复此楼» 本帖附件资源列表
-
欢迎监督和反馈：小木虫仅提供交流平台，不对该内容负责。
本内容由用户自主发布，如果其内容涉及到知识产权问题，其责任在于用户本人，如对版权有异议，请联系邮箱：xiaomuchong@tal.com - 附件 1 : 1ac7.data
2014-03-19 10:47:03, 1.21 M
» 猜你喜欢
小木虫没落了，除了祈祷帖子，几乎看不到有价值的帖子
已经有15人回复
-
面上的水很深
已经有18人回复
-
国社科通讯评审
已经有5人回复
-
5个%2F，非固定段22个字母
已经有9人回复
-
生命口C13面上会评时间
已经有11人回复
-
内心匮乏
已经有16人回复
-
生命口面上会评结束了吗大家有知道结果吗？现在还没有结果正常不？
已经有9人回复
-
投英文期刊如何查重
已经有6人回复
-
不要再数国自然申请书的 filecode 的分隔符个数了
已经有21人回复
-
伯胺上甲基求助
已经有7人回复
liuchenhan
新虫 (小有名气)
- 应助: 0 (幼儿园)
- 金币: 1536.5
- 散金: 4
- 帖子: 170
- 在线: 108小时
- 虫号: 1508714
- 注册: 2011-11-25
- 专业: 传热传质学
|
脚本文件如下： # Created by charmm2lammps v1.8.1 on Wed Mar 19 10:44:19 CST 2014 units real neigh_modify delay 2 every 1 atom_style full bond_style harmonic angle_style charmm dihedral_style charmm improper_style harmonic pair_style lj/charmm/coul/long 8 10 pair_modify mix arithmetic kspace_style pppm 1e-4 read_data 1ac7.data special_bonds charmm fix 1 all nve fix 2 all shake 1e-6 500 0 m 1.0 velocity all create 0.0 12345678 dist uniform thermo 1 thermo_style multi timestep 0.5 restart 10 1ac7.restart1 1ac7.restart2 dump 1 all atom 10 1ac7.dump dump_modify 1 image yes scale yes run 20 |
2楼2014-03-19 10:48:13
liuchenhan
新虫 (小有名气)
- 应助: 0 (幼儿园)
- 金币: 1536.5
- 散金: 4
- 帖子: 170
- 在线: 108小时
- 虫号: 1508714
- 注册: 2011-11-25
- 专业: 传热传质学
|
用下面的脚本试了好像可以，但还是有warning;大神帮忙解释一下吧，头痛啊。 WARNING: Inconsistent image flags (../domain.cpp:594) WARNING: Bond/angle/dihedral extent > half of periodic box length (../domain.cpp:667) 脚本： # Created by charmm2lammps v1.8.1 on Wed Mar 19 10:44:19 CST 2014 units real neighbor 5.0 nsq neigh_modify delay 2 every 1 atom_style full bond_style harmonic angle_style charmm dihedral_style charmm improper_style harmonic pair_style lj/charmm/coul/long 8 10 pair_modify mix arithmetic kspace_style pppm 1e-4 read_data 1ac7.data special_bonds charmm min_style cg minimize 0.0 1.0e-7 10000 100000 fix 1 all nve fix 2 all shake 1e-6 500 0 m 1.0 velocity all create 0.0 12345678 dist uniform thermo 1 thermo_style multi timestep 0.5 restart 10 1ac7.restart1 1ac7.restart2 dump 1 all atom 10 1ac7.dump dump_modify 1 image yes scale yes run 20 |
3楼2014-03-19 10:57:09
liuasia
铜虫 (小有名气)
- 应助: 0 (幼儿园)
- 金币: 102.6
- 散金: 200
- 帖子: 69
- 在线: 122.6小时
- 虫号: 3001880
- 注册: 2014-02-27
- 性别: GG
- 专业: 艺术美学
4楼2014-04-04 14:51:11
5楼2014-04-04 15:59:32
liuchenhan
新虫 (小有名气)
- 应助: 0 (幼儿园)
- 金币: 1536.5
- 散金: 4
- 帖子: 170
- 在线: 108小时
- 虫号: 1508714
- 注册: 2011-11-25
- 专业: 传热传质学
6楼2014-04-06 10:46:38
7楼2016-11-30 21:12:26
wl2009071613
新虫 (小有名气)
- 应助: 0 (幼儿园)
- 金币: 263.6
- 红花: 3
- 帖子: 144
- 在线: 21.9小时
- 虫号: 5041810
- 注册: 2016-09-21
- 性别: GG
- 专业: 纳米生物学
|
你好，我最近也是在做lammps的DNA模拟，之前用lammps自带例子运行，出现如下错误提示： =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 139 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES =================================================================================== YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11) This typically refers to a problem with your application. Please see the FAQ page for debugging suggestions 后来采用你修改的in文件和data文件，多了两个warning： WARNING: Inconsistent image flags (../domain.cpp:678) WARNING: Bond/angle/dihedral extent > half of periodic box length (../domain.cpp:799) =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 139 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES =================================================================================== YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11) This typically refers to a problem with your application. Please see the FAQ page for debugging suggestions 求指教  |
8楼2018-04-09 16:43:28
10