Dear Leila, The RMSD is, by default, calculated with respect to the coordinates in the tpr file, which is why you get different results with different tprs. Which one to choose depends on exactly what you want to measure.
Kind regards, Erik ______________________________ Erik Marklund, PhD Marie Skłodowska Curie INCA Fellow Department of Chemistry – BMC Uppsala Universtity erik.markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se> On 23 Jan 2017, at 17:10, leila karami <karami.lei...@gmail.com<mailto:karami.lei...@gmail.com>> wrote: Dear gromacs users, About the concatenation trajectory files, I have a question. I did 10 MD simulations (each section 10 ns). Now, I want to concatenate all of the trajectories and determine RMSD on whole trajectory. To do this, I used the following command: gmx trjcat -f md1.trr md2.trr md3.trr md4.trr md5.trr md6.trr md7.trr md8.trr md9.trr md10.trr -o all_md.xtc –settime The whole trajectory file made correctly. To determined RMSD, I used the following command. gmx rms -f all_md.xtc -s *.tpr -n index.ndx -o rmsd.xvg -tu ns I want to know, which tpr file must be used? tpr1 or tpr2 or tpr3 or …? I tried this command with md1.tpr and md10.tpr and in each time, RMSD had the different values. So, should I concatenate the tpr files and use the complete tpr file. How can I concatenate the tpr files? Best -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org<mailto:gmx-users-requ...@gromacs.org>. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
