Hi, I guess that the reported energy are averaged over the simulation time. If you want to compare energies and understand what change in the topology implied, it is better to compare the energies of the first step using the same starting structure.
The definition of LJ interactions (including 1-4 interaction) is not trivial and involved different parameters, I would suggest to check if your change in topology are doing what to desire by looking at http://manual.gromacs.org/documentation/current/reference-manual/topologies/topology-file-formats.html?highlight=pairs%20 with particular attention to values of gen-pairs, nrexcl, [pairs]. Best regards Alessandra On Thu, Feb 13, 2020 at 9:49 AM Luirink, R.A. <r.a.luir...@vu.nl> wrote: > Anyone has advice/feedback? > > On 06/02/2020, 16:55, "gromacs.org_gmx-users-boun...@maillist.sys.kth.se > on behalf of Luirink, R.A." < > gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of > r.a.luir...@vu.nl> wrote: > > Here some output to illustrate what I mean. This is what you would > expect and what I also get for standard atom-atom interactions, not 1-4 and > not specified in pairs. LJ-SR and Coul-SR but not LJ-14 and Coul-14 > > Energy Average Err.Est. RMSD Tot-Drift > > ------------------------------------------------------------------------------- > Coul-SR:CXD-CDLAL 0.0134301 0.0035 0.00986618 0.0226416 > (kJ/mol) > LJ-SR:CXD-CDLAL -0.0871943 0.017 0.0466035 -0.109977 > (kJ/mol) > Coul-14:CXD-CDLAL 0 0 0 0 > (kJ/mol) > LJ-14:CXD-CDLAL 0 0 0 0 > (kJ/mol) > > This is what you would expect for 1-4 interactions (which I get for > standard 1-4 interactions, but not the ones I specified) not LJ-SR and not > Coul-SR but LJ-14 and Coul-14: > Coul-SR:CXN-CDLAL 0 0 0 0 > (kJ/mol) > LJ-SR:CXN-CDLAL 0 0 0 0 > (kJ/mol) > Coul-14:CXN-CDLAL 0.716966 0.00016 0.0100767 > -1.69012e-05 (kJ/mol) > LJ-14:CXN-CDLAL -0.222359 7.1e-05 0.00496677 > -7.03428e-05 (kJ/mol) > > And this is what I get for my specified pairs BOTH LJ-SR and Coul-SR > as LJ-14 and Coul-14: > Coul-SR:CXZ-CXD 0.674878 0.11 0.276414 0.758962 > (kJ/mol) > LJ-SR:CXZ-CXD 0.373275 0.32 1.01553 2.06088 > (kJ/mol) > Coul-14:CXZ-CXD 4.53861 0.2 0.46893 1.30594 > (kJ/mol) > LJ-14:CXZ-CXD 0.186637 0.16 0.507767 1.03044 > (kJ/mol) > > It seems like a bug to me, or I have overlooked something.. > > On 06/02/2020, 14:44, " > gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Luirink, > R.A." <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of > r.a.luir...@vu.nl> wrote: > > Gromacs version 2018.6 btw. > > On 06/02/2020, 13:54, " > gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Luirink, > R.A." <gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of > r.a.luir...@vu.nl> wrote: > > What I have tried is, instead of adding them to the [ pairs ] > block, is change the epsilon value manually via the [ nonbon_params ] > block. However, I can’t manually change the electrostatic interactions to > account for the fudgeQQ (0.8333) for these specific pairs (or at least, I > haven’t found a way to do so). > > > From: "Luirink, R.A." <r.a.luir...@vu.nl> > Date: Thursday, 6 February 2020 at 11:49 > To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org> > Subject: specified [ pairs ] and now get both LJ_SR and LJ_14 > as energy output > > Hello, > I try to specify a pair of atoms to be treated as a 1-4 > interaction (I replaced a covalent bond to a soft core restraint for free > energy calculation purposes, and now gromacs does not recognize it anymore > as 1-4 interaction, but it should still be treated as such). > I added the pair to the [ pairs ] block in the topology. I did > the same for 1-3 interactions, where I set the parameters to 0 for LJ > interactions. > > When I check the energy between these pairs of atoms, I > indeed get a value for LJ_14. However, my LJ_SR value is non-zero (and > exactly twice the average value of LJ_14, where I have a fudge of 0.5). How > can I fix this issue? > Best, > Rosa > -- > 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. -- 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.
