Allright Sir Thank you very much for clearing the point. With Regards Suniba
Sent from my iPhone > On 15-May-2016, at 12:14 pm, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > > Hi Suniba, > > No, you will get the stability of configuration in the order parameters you > choose. But you don't know how much conformational freedom you have at each > point. Low RMSD will mean stable, but a fixed point at high RMSD does not. > Also note that the Rg is sort of part of the RMSD, which can be written as > Rg(A)+Rg(B)-2S(A,B), where S is the similarity. So these order parameters > will be correlated. > > Cheers, > > Tsjerk > >> On Sun, May 15, 2016 at 8:13 AM, sun <sun.i...@gmail.com> wrote: >> >> 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. > > > > -- > 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.