| 查看: 1107 | 回复: 1 | ||||
| 本帖产生 1 个 模拟EPI ，点击这里进行查看 | ||||
smutao禁虫 (著名写手)
|
[交流]
[smutao文集-自编教程]如何快速构建单链Polymer模型？ 已有1人参与
|
|||
|
最近做了一点和polymer有关的工作，想到了一个快速构建单链polymer的方式。 希望对大家有帮助。 Sometimes, when we need to do some research on polymers using the MD simulation methods, we have to construct models of them first. It is a common way to construct such models using commercial software packages such as Material Studio, Discovery Studio and so forth. But what can we do without them? The main tool we need to construct such models is Open Babel. Following is the protocol: 1. Get the structure information of the polymer you study(usually the 2D structure); 2. Draw a short sample of the polymer in Chemdraw saving as ".cdx" file or 3D modeling software such as GaussView saving as ".mol2" file; 3. Using Open Babel to convert the ".cdx" or ".mol2" file into SMILES format; 4. Look at the SMILES string and learn how it is organized; 5. Write the SMILES string for the polymer you study; 6. Using Open Babel to convert the SMILES format into a ".mol2" file. So the raw model has been constructed. However, there are a little problems before using it for MD simulation. Firstly, there will be same atom names, and we have to adjust them to avoid conflicts. Secondly, no other problems found... :-) Enjoy! |
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 : How_To_Construct_A_Polymer_Model.pdf
2014-06-11 10:21:37, 93.36 K
» 收录本帖的淘帖专辑推荐
 amber |
» 猜你喜欢
材料调剂
已经有4人回复
-
304求调剂
已经有14人回复
-
求调剂
已经有24人回复
-
一志愿华东理工085601材料工程303分求调剂
已经有7人回复
-
288环境专硕,求调材料方向
已经有25人回复
-
0703化学
已经有25人回复
-
求调剂 一志愿西南交通大学085701环境工程 282分
已经有12人回复
-
一志愿211，化学学硕，310分，本科重点双非，求调剂
已经有3人回复
-
一志愿211，0703化学305分求调剂
已经有12人回复
-
一志愿211，化学学硕，310分，本科重点双非，求调剂
已经有4人回复
pigrass
专家顾问 (著名写手)
伊卡斯特的小猪
-
专家经验: +503 - 模拟EPI: 4
- 应助: 377 (硕士)
- 金币: 10371
- 散金: 3286
- 红花: 166
- 帖子: 2101
- 在线: 1968.4小时
- 虫号: 1463681
- 注册: 2011-10-27
- 性别: GG
- 专业: 高分子材料结构与性能
- 管辖: 分子模拟
2楼2014-06-11 17:55:15
