As far as i know NO. You want the adsorption energy which needs an accurate sampling of protein in different distances and calculating energy for each sample and then .... BTW, i think calculating this quantity for a big molecule like protein is not a great idea. I think you need to do long time simulation and then find out which residue/s are closer to nanotube most of the time and calculate interaction energy or for more real adsorption energy cut that residue/s and use umbrella sampling...
Rose On Sat, 29 Sep 2018, 10:27 Sundari, <sundi6...@gmail.com> wrote: > Hi, > Is there any other way for example calculation of binding energy by my > existed files (normal MD .trr and .edr files) generated by gromacs instead > of restart a simulation. Because currently I am not familiar with the > umbrella sampling and have urgent need of energies. > Please suggest any idea. > > sundari > > > > > On Fri, Sep 28, 2018 at 8:47 PM rose rahmani <rose.rhm...@gmail.com> > wrote: > > > Hi, > > > > You can calculate adsorption energy by umbrella sampling. > > http://www.mdtutorials.com/gmx/umbrella/index.html > > .edr just gives you the interaction energy not adsorption energy and > > distance. > > > > Rose > > > > On Fri, Sep 28, 2018 at 6:37 PM Sundari <sundi6...@gmail.com> wrote: > > > > > Dear Gromacs users, > > > > > > I want to calculate Binding energy between the protein and the carbon > > nano > > > tube. Is there any way to do that by gromacs commands. > > > As I only have .xtc and .tpr files from gromacs. > > > > > > Please suggest me any idea or any article so that based on trajectories > > > (xtc or trr) how one can get these binding energies. > > > > > > Regards, > > > Sundar > > > -- > > > 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. > > > -- > 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.