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
  • 3.10 host guest 2
    # 4090 /home/data/zzy/koff/smd/host-guest/test1 cp /home/data/zjhan/diffusion_calculation/aspirin/box_50/npt/npt.gro ./ cp /home/data/zjhan/diffusion_calculation/aspirin/box_50/gmx.top ./ cp /home/
    MD 2025-03-10 19:57:19    zhouzhaoyin
  • 3.10 host guest
    v100的轨迹正在转移至4090，转移完成后删除v100的数据（300G） # 4090 /home/data/zzy/koff/smd/host-guest/test1 cp /home/data/zjhan/diffusion_calculation/aspirin/box_50/npt/npt.gro ./ cp /home/data/zjhan/diffusion_calculat
    MD 2025-03-10 19:50:11    zhouzhaoyin
  • 3.6 jarzynski PMF
    85.9 /home/databank/zzy/project/smd/hiv-1/smd3/jarzynski-pmf/B439-test/jarzynski-PMF-test.ipynb 晚上经师姐指导，不该对W进行积分，就是要算随着cv，W的变化，那其实就是每一个 dx 算一个W就好 SMD就是用来获取解离路径，预测大致的过渡态，每一个极大值点一般上对应着关键相互作用的破坏 输入数据 8
    MD 2025-03-08 21:49:51   
  • 3.5 jarzynski PMF
    输入数据 85.9 v100 单次SMD模拟测试 # 85.9 /home/databank/zzy/project/smd/hiv-1/smd3/jarzynski-pmf/test cp ../../10_repeat_v_0.01/B439/1/ xvg ./ sed '/^#/d' smd_pullx.xvg|sed '/^@/d' |awk '{print $1}' >times
    MD 2025-03-06 22:10:29    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 2025-03-06 15:23:54    zhuziyu
  • 2.26 smd+jazynsiki
    On the spontaneous encapsulation of proteins in carbon nanotubes - ScienceDirect 公式很清晰 先计算SMD模拟中对配体施加的不可逆功再通过多个不可逆功+jarzynski得到PMF 数据整理 # 85.9 /home/databank/zzy/project/smd/hiv-1/smd2/analysis/f
    MD 2025-03-01 17:04:30    zhouzhaoyin
  • 3.1 hiv smd
    根据2.24，2.25与朱老师，乐云师姐的讨论 想做一个 “错误”初始构象出发的SMD模拟 10:44 提交hermite constraint dock 任务，ref 为 B439的smina对接结果，与晶体结构差距较大，如下图：蓝色为B409晶体结构构象，黄色为B439 hermite CD构象，红色为B439 smina dock构象 任务完成后，要gv-check，考虑等待流程化脚
    MD 2025-03-01 10:49:53    zhouzhaoyin
  • 1.31 smd+jazynsiki sob
    科音-卢天 27：28 提到他本人还是其他人做过 smd+jazynsiki 算pmf的工作，可借鉴
    MD 2025-02-26 19:58:18    zhouzhaoyin