Desmond Configuration in Cluster

袁曙光 2011-7-16 13:17

Configure the schrodinger.hosts in /home/user/.schrodinger folder 1. with multiple nodes in the same host name: 32a host: myhost queue: PBS qargs:&n ...

个人分类: 科研笔记|3888 次阅读|没有评论

Membrane Protein Simulation with Desmond

热度 1 袁曙光 2011-6-25 02:59

Desmond supports algorithms typically used to perform fast and accurate molecular dynamics. Long-range electrostatic energy and forces can be calculated using particle-mesh-based Ewald techniques.Constraints can be enforced using the M-SHAKE algorithm. These approaches can be used in combination w ...

个人分类: 科研笔记|8284 次阅读|1 个评论 热度 1

humor at conference

热度 2 袁曙光 2011-5-24 21:22

Recently, I am attendinga conference in Utrecht, Netherlands. Some speakers (PhD student)made mistakes during the presentation. Although scientists are quit serious for most cases, they still have humors: 1. one speaker madespellingmistakes for his institut ...

个人分类: 科研笔记|2850 次阅读|6 个评论 热度 2

Science Arts

热度 3 袁曙光 2011-5-22 20:11

Protein-ligand interaction Membrane protein Induced Fit docking

个人分类: 科研笔记|4466 次阅读|1 个评论 热度 3

Is 5Å big enough for your docking grid box?

袁曙光 2011-5-12 03:04

Recently, I am preparing a manual script for previous work. When someone read it he claimed in the email: "your gird box for docking is too small to include the whole molecule. I measure the distance between two atoms in the ligand and it is11 Å , but you defined y ...

个人分类: 科研笔记|3401 次阅读|没有评论

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