VMD-L Mailing List

From: sunyeping (sunyeping_at_aliyun.com)
Date: Wed Apr 02 2014 - 10:40:07 CDT

Dear Felipe,In VMD TkConsole I type pbc unwrap, the resulting structures become better but there are still many bonds that look very crazy. I don't know how trjconv works here. I have tried: trjconv -f input.xtc -o output.xtc -pbc moltrjconv -f input.xtc -o output.xtc -pbc unjumptrjconv -f input.xtc -o output.xtc -ur compactBut they all didn't work.By typing pbc box -on, I find the PBC box didn't overlap with water box. Could you give me more explanation to help me solve this question? Thanks a lot Yeping ------------------------------------------------------------------ 发件人：Felipe Merino <felipe.merino_at_mpi-muenster.mpg.de> 发送时间：2014年4月2日(星期三) 04:45 收件人：孙业平 <sunyeping_at_aliyun.com> 主　题：Re: vmd-l: visualize gromacs trajectory in vmd The frames come wrapped around the cell. You need to reimage things in order to get a reasonable picture. I am not sure if the pbc tools inside vmd can handle directly the xtc file but definitely you can do it with trjconv Felipe On 04/01/2014 05:43 PM, sunyeping wrote: Dear all, I am trying to visualize gromacs trajectory in VMD. when I load my .gro file, the GUI window of VMD show a structure that seems to be correct. However, when I load .xtc or .trr file, the strucute shown is seriously deformed. Most bonds become very long and the structures looks very strange. Could anyone tell me how to show the trajectory correctly? Thanks. Yeping Sun Institute of Microbiology, Chinese Academy of Sciences