回复： Re: [gmx-users] how to remd analysi?

[xi zhao]

 I performed remd using GROMACS 3.3.1 at four different temperatures: 270k, 400k, 540k, 660k, and produced four trajectories. I want to know whether my simulation is ok, but I do not know how to analysis my trajectories. Though I have demux.pl script and produced replica_index.xvg and replica_temp.xvg files, the contents of two files are the same! I use trjcat_d to produce a continuous trajectory,according to wiki gromacs. In fact,  for a REMD simulation, I can not judge whether the simulations is ok , and if they are ok, how to further analyze or  extract useful information from trajectories! Are you clear?
  Thank you for your help!   

Mark Abraham <Mark.Abraham at anu.edu.au> 写道：
  xi zhao wrote:
> Dear all users:
> I performed remd using GROMACS 3.3.1,but I find that I do not know how 
> to analyze the result further,

"Analyze" really doesn't tell us what you're trying to do.

> though I have demux.pl script and produced 
> replica_index.xvg and replica_temp.xvg files, the contents of two files 
> are the same! I use trjcat_d to produce a continuous trajectory,when 
> analyzing the trajectory, the system shows segment fault? Please give me 
> some advice and analysis tools!

You need to tell us what you're trying to do explicitly. That means text
describing your intentions, a command line that you tried to use, the
output from it, and (potentially) why you think it wasn't what you expected.

A segmentation fault is a generic problem with referencing an illegal
memory location, and thus just about anything could cause it. If there's
no GROMACS-specific error message, though, then it's very likely to be
something you've done wrongly.

Mark
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