ACEMD入门：利用HTMD进行项目实践

序

前面几篇介绍了ACEMD的安装、入门使用以及可视化，本文将综合前面的内容，实战一个小的分子动力学项目。

Projections in HTMD

#!/usr/bin/python3

# coding: utf-8

# In[1]:导入模块，开启可视化

from htmd.ui import *

config(viewer='webgl')

%pylab inline

# In[2]:交互式可视化轨迹

mol = Molecule('ntl9_structure.pdb')

mol.read('ntl9_trajectory.xtc')

mol.filter('protein')

mol.view()

# In[3]:可视化PDB

crystal = Molecule('ntl9_crystal.pdb')

crystal.view()

# In[4]:计算rmsd,并绘图

metr = MetricRmsd(crystal, 'protein and name CA')

proj = metr.project(mol)

plt.plot(mol.fstep*np.arange(len(proj)), proj)

_ = plt.xlabel('Time (ns)')

_ = plt.ylabel('RMSD to crystal')

# In[5]:获取项目的simlist

sims = simlist(glob('datasets/1/filtered/*/'), 'datasets/1/filtered/filtered.pdb')

metr = Metric(sims)

metr.set(MetricDistance('protein and name CA', 'resname MOL and noh', metric='contacts'))

data = metr.project()

data.fstep = 0.1

# In[6]:Working with data maps

print(data.dat[14].shape)

# In[7]:获取map头部数据

# In[8]:建立mapping，获取其头部数据

mapping = MetricSelfDistance('protein and name CA').getMapping(mol)

mapping.head()

# In[9]:索引pandas数据框

# In[10]:使用数据框索引

# In[11]:获取map特定位置数据

data.map['description'][20]

参考资料

https://software.acellera.com/docs/latest/htmd/tutorials/projections.html

http://gainstrong.net/works/hudong/

https://software.acellera.com/docs/latest/htmd/tutorials/htmd-molecules.html

https://software.acellera.com/docs/latest/htmd/tutorials/visualization.html