Re: [AMBER] dimer rmsd issue.

From: Bill Ross <>
Date: Sun, 14 May 2017 12:16:55 -0700

There is a reasonable chance that your dimer has been reimaged if you
used iwrap=1, so you would need to reimage the trajectory. Looking at it
in VMD will answer that question.


On 5/14/17 10:13 AM, Saman Yousuf ali wrote:
> Dear All,I have plotted dimer rmsd using following command;parm *.prmtoptrajin md_simulation?.mdcrdtrajin md_simulation??.mdcrdautoimagestrip :Na+,WAT outprefix nowater
> rms first out rmsd.dat :1-534.C,CA,Ntrajout netcdf
> I also tried another command which was suggested in amber archive ( to improve rmsd;
> parm *.prmtoptrajin md_simulation?.mdcrdtrajin md_simulation??.mdcrdcenter :1-267 mass origin
> image origin center familiarcenter :1-534 mass originimage origin center familiarstrip :Na+,WAT outprefix nowaterrms first out rmd.dat :1-534.C,CA,Ntrajout netcdf
> got same result. RMSD plot image attached here. Does anybody know how I might fix the RMSD values Any suggestion would be really appreciated.
> Thanks
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Received on Sun May 14 2017 - 12:30:02 PDT
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