[gmx-users] Water removed from system and visualizing protein alone in VMD. But problem in visualization of all frames

sun sun.iba2 at gmail.com
Thu Feb 4 19:20:40 CET 2016

Hello Everyone
I have performed a md simulation if protein in water for 10ns and frames were obtained after every 10ps. I wanted to visualize the.gro and trajectory file in VMD, without water, so I prepared an index file containing protein only. Using editcon i removed water from md.gro as well but I loaded the files in VMD, 1000 time frames are loaded but I cannot see any change in structure or per frame conformation. The protein is still. I am not clear what to do. I tried keeping water in .trr and then in .gro and repeated steps but no results. When I use original .trr and .gro, only then i visualize the change in structure. Please help me


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