[gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output

Thu Feb 13 09:48:48 CET 2020

Anyone has advice/feedback?

On 06/02/2020, 16:55, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Luirink, R.A." <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of r.a.luirink at 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-bounces at maillist.sys.kth.se on behalf of Luirink, R.A." <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of r.a.luirink at vu.nl> wrote:

        Gromacs version 2018.6 btw. 

        On 06/02/2020, 13:54, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of Luirink, R.A." <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf of r.a.luirink at 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.luirink at vu.nl>
            Date: Thursday, 6 February 2020 at 11:49
            To: "gmx-users at gromacs.org" <gmx-users at 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
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