i have generated trr file for a protein containing two chains .during the simulation two chains are going at two different sides of the box. so the RMSD results are abruptly high (near 35-40 angstrom). To create a image of one chain at the same side of other chain,i used the following command by removing pbc ============== try1. trjconv -s .tpr -f .trr -o .xtc -pbc mol -ur compact try2.trjconv -s tpr -f .trr -o .xtc -pbc nojump try3. -f a.mdp -c a_cluster.gro -o a_cluster.tpr try4 trjconv -s a.tpr -f .trr -o xtc -fit rot+trans ============================== still similar results are coming. but for each chain,RMSD value is reasonable. kindly suggest some way to calculate RMSD value for full protein
On Wed, Oct 30, 2019 at 4:59 PM rajat punia <rjtpu...@gmail.com> wrote: > make sure you superimpose the structures using -fit flag. > > > On Wed, 30 Oct 2019 at 16:39, shakuntala dhurua <madhu.dhuru...@gmail.com> > wrote: > > > actually I am using insulin protein system, i have calculated rmsd but > that > > is too high which is approx 40 amstrong which is not supposed to be , and > > initially during energy minimization two chain go far away from each > other. > > I have used flag like trjconv -s .tpr -f .trr -o .xtc -pbc mol -ur > compact > > trjconv -s .tpr -f .trr -o .xtc -pbc nojump etc but still result is same > . > > so please suggest me to solve this problem. > > -- > > 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. > > > > > -- > *Regards,* > *Rajat Punia* > *PhD Chemical Engineering* > *IIT Delhi* > *+91-9821210386* > -- > 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. > -- 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.