zhouzhaoyin

zhouzhaoyin @zhouzhaoyin

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组织

@analoguecomputation 模拟计算 @wlzhu_team 课题组公共空间 @trip13 trip13 @srse 科研小技能交流
  • record
    conda create -n gcc_8_5 gxx_linux-64=8.5.0 gcc_linux-64=8.5.0 sysroot_linux-64=2.17 python=3.8 openmpi 安装后输出： For Linux 64, Open MPI is built with CUDA awareness but this support is disabled by defa
    MD 2024-05-14 13:47:02    zhouzhaoyin
  • 5.14 install conda
    # Index of /anaconda/archive/ | 清华大学开源软件镜像站 | Tsinghua Open Source Mirror 下载 wget https://mirrors.tuna.tsinghua.edu.cn/anaconda/archive/Anaconda3-5.2.0-Linux-x86_64.sh 实际用的时候，报错 2024-05-14 01:23:4
    MD 2024-05-14 13:02:07    zhouzhaoyin
  • pymol
    generate dimer from a monomer fetch 4ryl symexp 4ryl, 4ryl, 4ryl, 3 references and materials: protein structure - Generate full dimer from monomer with C2 symmetry? - Biology Stack Exchange How ca
    share 2024-05-11 10:42:32    zhouzhaoyin
  • MD
    using blast to check your sequence after preparation! Implicit solvent model mdp file (amber GB)
    share 2024-04-30 09:36:53    zhouzhaoyin
  • data analysis
    glide sdconvert -imae lig_epikout.mae -osdf lig_epikout.sdf
    share 2024-04-30 09:00:34    zhouzhaoyin
  • 0425
    实际需求： 给定一个 temp, top ， example.mdp 自动流程化调参 gmx_mpi make_ndx -f npt2.gro -o index.ndx for aa in $(seq 1 $num_replica) do b=`sed -n "${aa}p" ${file_dir}/temp` mkdir -p ${input_dir}/md${aa} sed "
    MD 2024-04-26 14:34:40    zhouzhaoyin
  • MD流程(GMX)
    1. 生成拓扑文件 gmx_mpi pdb2gmx -ignh -ff amber99sb-ildn -f 1udt-clean.pdb -o fws.gro -p fws.top -water tip3p # 我们得到了三个输出文件: 结构文件.gro, 拓扑文件.top, 位置限制文件posre.itp. 2. 模拟体系构建（添加模拟盒子并溶剂化） ## 添加模拟盒子 gmx_m
    share 2024-04-24 10:17:49    zhouzhaoyin
  • research
    结合自由能（Absolute binding free energy, ABFE）计算和相对结合自由能（Relative binding free energy, RBFE）计算，前者常用于配体与受体结合前后状态的估算，后者常见于靶点与不同配体结合状态下的估算。
    share 2024-04-24 09:01:57    zhouzhaoyin