Re: [AMBER] dimer rmsd issue.

From: Elvis Martis <>
Date: Sun, 14 May 2017 17:44:13 +0000

did you have a look at your trajectories using an visualizer???

Perhaps VMD or chimera can be helpful.

                   Best Regards


Elvis Martis
Ph.D. Student (Computational Chemistry)
 at Bombay College of Pharmacy

A Kalina, Santacruz [E], Mumbai 400098, INDIA
Skype. adrian_elvis12<>


From: Saman Yousuf ali <>
Sent: 14 May 2017 22:43:54
To: AMBER Mailing List
Subject: [AMBER] dimer rmsd issue.

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.


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