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