[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
Tue Feb 18 14:36:28 CET 2020
Thank you Alessandra,
They are indeed averaged over the simulation time, but the SR values should be zero for these specific pairs of interactions.
I managed to "hack" it by defining a bond between them with a force constant of zero.
It works!
Best,
Rosa
Op 17-02-20 10:15 heeft gromacs.org_gmx-users-bounces at maillist.sys.kth.se namens Alessandra Villa <gromacs.org_gmx-users-bounces at maillist.sys.kth.se namens alessandra.villa.biosim at gmail.com> geschreven:
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.luirink at vu.nl> wrote:
> 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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