VMD-L Mailing List

From: sunyeping (sunyeping_at_aliyun.com)
Date: Mon Apr 07 2014 - 06:52:55 CDT

Dear Felipe,The command trjconv -f input.xtc -o output.xtc -s topology.tpr -ur compact -pbc mol -center  works.Thank you. Yeping Sun Institute of Microbiology, Chinese Academy of Sciences ------------------------------------------------------------------ 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) 23:47 收件人：孙业平 <sunyeping_at_aliyun.com> 抄　送：vmd-l <vmd-l_at_ks.uiuc.edu> 主　题：vmd-l: Re: RE：vmd-l: visualize gromacs trajectory in vmd I think this is getting a bit off topic for this list, but the command with trjconv should be trjconv -f input.xtc -o output.xtc -s topology.tpr -ur compact -pbc mol -center or something in those lines Best Felipe On 04/02/2014 05:40 PM, sunyeping wrote: 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 mol trjconv -f input.xtc -o output.xtc -pbc unjump trjconv -f input.xtc -o output.xtc -ur compact But 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