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

[David van der Spoel]

xi zhao wrote:
>  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!   

read your output file (md.log).
view the xvg files.
then come back with more directed questions.


> 
> */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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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se