[gmx-users] specified [ pairs ] and now get both LJ_SR and LJ_14 as energy output
Luirink, R.A.
r.a.luirink at vu.nl
Thu Feb 6 16:53:58 CET 2020
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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