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VMD 使用说明

VMD介绍

VMD是分子可视化软件,主要用以查看分子动力学轨迹,

官网: http://www.ks.uiuc.edu/Research/vmd/

VMD安装

Linux 和 Windows

直接查看官网,其他无需特殊注意

MacOS Catalina版本以上

由于苹果不再支持32位的软件,因此需要64位版本的VMD。

已经编译好的软件从这里下载: https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/31222.html

使用集群的VMD进行远程查看

现在51和52集群上均安装了VMD/1.9.3

使用方法是

module load vmd/1.9.3

然后如同在本地端使用vmd一样使用即可。

集群打开vmd报错

如果遇到报错

XRequest.149: BadMatch (invalid parameter attributes) 0xa00105
XRequest.149: GLXBadContext 0xa00001

首先在集群上查看

glxinfo
glxgears

如果得到报错

name of display: localhost:24.0
libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: swrast
X Error of failed request:  GLXBadContext
  Major opcode of failed request:  149 (GLX)
  Minor opcode of failed request:  6 (X_GLXIsDirect)
  Serial number of failed request:  23
  Current serial number in output stream:  22

libGL error: No matching fbConfigs or visuals found
libGL error: failed to load driver: swrast
X Error of failed request:  BadValue (integer parameter out of range for operation)
  Major opcode of failed request:  149 (GLX)
  Minor opcode of failed request:  3 (X_GLXCreateContext)
  Value in failed request:  0x0
  Serial number of failed request:  28
  Current serial number in output stream:  30

那么请在本地Mac/iMac的终端上退出XQuartz然后在本地终端里输入:

defaults write org.macosforge.xquartz.X11 enable_iglx -bool true 

即可解决问题

Ref: https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/28494.html