VMD-L Mailing List

From: Felipe Merino (felipe.merino_at_mpi-muenster.mpg.de)
Date: Wed Apr 02 2014 - 10:47:30 CDT

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
>
>
>