Thank you very much Sir. I get you. Is it good enough to probe the stability of complex by projecting any two variables with free energy? like RMSD and Rg?
Sent from my iPhone > On 15-May-2016, at 10:51 am, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > > Hi Suniba, > > No, with gmx anaeig you can select -2d, which does a 2D projection onto the > selected eigenvectors. Alternatively, you can combine any two projections > onto eigenvectors, which you get using the option -proj. The quickest way > to do that is something like: > > paste <(grep -v '^[@#]' proj1.xvg) <(proj2.xvg) | awk '{print $2, $4}' > > combined.xvg > > You will loose the labels, but that should be fine. > > You can combine other variables in a similar manner. > > Hope it helps, > > Tsjerk > >> On Sun, May 15, 2016 at 5:33 AM, sun <sun.i...@gmail.com> wrote: >> >> Hello everyone >> I am using Gromacs 5.0 for protein-ligand MD. I want to do FEL analysis >> for the stability of my pro-lig complex. In a 2015 paper, The group >> calculated two principal component, PC1 and PC2 and then prepared an.xvg >> file to be used as input for g_sham. My question is, when we use g_anaeig; >> we get eigenvec.xvg. from -comp flag. Now how shall one select two >> principal components from that data? I am sorry if my question is wrong but >> please help me. >> >> My second question is, can we use any two parameters like rmsd and Rg for >> input in g_sham to probe the stability of complex? Is that valid? >> >> With Regards >> Suniba >> >> Sent from my iPhone >> -- >> 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. > > > > -- > Tsjerk A. Wassenaar, Ph.D. > -- > 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.