zhouzhaoyin

zhouzhaoyin @zhouzhaoyin

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  • vsREMD 操作
    确定需要的vsREMD副本数 Temperature generator for REMD-simulations (virtualchemistry.org) /home/databank/zzy/usp18/vsREMD/noloop_24/parameters 初始结构准备 注1：若是每个副本构象不同，可参考该流程，若初始结构完全一致，可跳转至“vsREMD测试”部分 注2
    share 2025-09-05 15:54:30    zhouzhaoyin
  • MD Operation
    Written in front Please remember that this is a very rough tutorial (honestly, I’m somewhat ashamed to call it a tutorial because it’s too rough). The only purpose of this "tutorial" is to help you na
    share 2025-09-04 13:18:39   
  • 进度汇总
    体系挑选 体系准备 v100 /home/databank/zzy/project/D3PM 0707 v100 /home/databank/zzy/project/D3PM/0630 # 对应的5对体系已完成准备,tpr已生成（75.3） MD任务 75.3 /home/data/zyzhou/project/D3PM/0630-5apo-system/1um_cmd/
    MD 2025-09-02 17:54:23    zhouzhaoyin
  • jupyter notebook
    windows cmd : ssh 172.21.85.24 linux server: jupyter notebook --no-browser 85.2 # 生成密码 jupyter notebook password # 查看密码加密形式 cat /home/dddc/.jupyter/jupyter_server_config.json vi ~/.ju
    share 2025-08-29 18:50:47    zhouzhaoyin
  • 8.19 batch3
    体系挑选 讨论 有三个体系暂且不做 蛋白检查 & 清洗 PDBfixer 75.5 /home/databank/zyzhou/project/d3pm/batch3/protein_preparation # 将需要下载的pdb id 上传pdb网站，进行批量下载，解压后 # 文件放于/home/databank/zyzhou/project/d3pm/b
    MD 2025-08-25 10:44:33    zhouzhaoyin
  • gmx2024
    env 4090 source /home/dddc/zzy/env/gmx-2024.4-gpu.sh v100 source ~/zzy/gmx2024.4-gpu.sh 75.4 与75.5、75.6相似，安装过程不赘述 由于该服务器从conda转向miniforge，openmpi lib位置变化，调用gmx前要 export LD_LIBRARY_PATH=/home/dddc/z
    MD 2025-08-25 10:35:17    zhouzhaoyin
  • interaction analysis
    PLIP - Help (tu-dresden.de) Non-covalent interactions between proteins and ligands pymol pi-pi set ray_shadows,0 create 8bcovbond, sele select a1, sele select a2, sele bond a1,a2 pseudoatom
    share 2025-08-21 14:21:26    zhouzhaoyin
  • gmx
    HIS/HID/HIP 科学网—#笔记#氨基酸残基质子化形式的判断（pKa预测） - 王少许的博文 (sciencenet.cn) make_ndx gmx_mpi make_ndx -f ref.pdb -o index.ndx > r 172-324 > r 49 57 58 233 333 334 336 349 389 393 rms nohup sh -c 'for
    share 2025-08-21 10:47:38    zhouzhaoyin