Thank you Justin. Using energy groups is not really that bad.
By using gmx select ‘atomname Cx and resname ADSORBATE and within 0.5 of resname SURFACE’ -on near.ndx I can find the atom/s of the adsorbate that is proximal to the surface and can track the LJ pot’l by frame and use VMD for further analysis Paul > On Apr 11, 2019, at 5:57 PM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 4/11/19 5:39 PM, paul buscemi wrote: >> Thank you for the response, Mark. >> >> I do use the rerun tactic, and this is not too bad for a small number of >> molecules >> >> but is there a way to include the index information within the mdrun (rerun >> ) … something like >> >> gmx mdrun -s adsorb.ener_gp.tpr -rerun adsorb,npt.trr - n use_only.ndx ? >> >> or use the indices within the grompp command ? >> > > The only solution is what Mark proposed - create a .tpr file with the > required energygrps and use mdrun -rerun. mdrun does not accept an index file. > > -Justin > >> Paul >> >>> On Apr 11, 2019, at 1:48 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: >>> >>> Hi, >>> >>> You can't do that with gmx energy, as you need mdrun to understand the new >>> grouping. But making a new .tpr with the energy groups so defined permits >>> you to use gmx mdrun -rerun for such a single point energy evaluation. >>> >>> Mark >>> >>> On Wed., 10 Apr. 2019, 22:24 p buscemi, <pbusc...@q.com> wrote: >>> >>>> Dear Users, >>>> I've performed an adsorption experiment in which a fraction of molecules >>>> in solution adsorb to a surface. I can extract the index of those adsorbed, >>>> and I can obtain the total interaction ( LJ ) of the energy group with the >>>> surface. >>>> I can estimate the average interaction of the adsorbed molecules by >>>> dividing the total energy by the number of molecules within a certain >>>> distance ( the index number ) >>>> How might I use gmx energy to recalculate the interaction using the >>>> original surface but only the adsorbed molecules specified in the index >>>> file... something like >>>> "gmx energy -f starting.gro -n index.ndx" >>>> >>>> A single point calculation would be quite satisfactory. >>>> thanks >>>> Paul >>>> -- >>>> 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. > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Office: 301 Fralin Hall > Lab: 303 Engel Hall > > Virginia Tech Department of Biochemistry > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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.