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.
Bill
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 AD-chain_complex-reimaged-20ns.nc netcdf
> I also tried another command which was suggested in amber archive (http://archive.ambermd.org/201109/0749.html) 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 AD-chain_complex-reimaged-20ns.nc 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
> |
> |
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun May 14 2017 - 12:30:02 PDT
