[gmx-users] SETTLE vs. LINCS -- different final energies of energy minimized structures

[Rakesh Sharan]

Thanks Justin and Mark!

I am sorry for not being clear. Actually I am taking configurations from an
equilibrated MD trajectory and minimizing these configuration using two
constraints -- LINCS and SETTLE. So, basically my initial starting
configuration is exactly same for each minimization (using SETTLE and
LINCS), but in few cases final energy of the minimized configurations are
different (in one case its -29146 and -29288 kj/mol) depending on the
choice of constraint algorithm used.

During energy minimization, for few configurations, in case of SETTLE I am
getting warning "Water molecule starting at atom 1893 can not be settled"
and in case of LINCS 4-5 warnings like "bonds that rotated more than 30
degrees" (runs are not crashing).

Mark, actually I am interested in the structural features of energy
minimized (or inherent) structures. This is the reason that I want to make
sure that I have properly energy minimized structures.

Best,
Rakesh

----------------------------------------------------
Rakesh S. Singh, Ph.D.
Postdoctoral Research Associate,
Department of Chemical & Biological Engineering,
Princeton University,
Princeton, NJ 08544 (US).


On Mon, Apr 18, 2016 at 12:24 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> I would further speculate that these differences are not even significant.
> You can also try rotating the whole system with gmx editconf before you
> generate the EM input, and that will be enough to change the order of  the
> floating point arithmetic, so that a different final energy minimum will be
> found. I don't know offhand what range of energy values you might expect,
> but you already have some related data for that, from your multiple EM runs
> from different starting points.
>
> I'm also sceptical about whether anything useful can be observed; the
> potential energy surface is only somewhat relevant to the properties of the
> thermalized ensemble.
>
> Mark
>
> On Mon, 18 Apr 2016 18:12 Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 4/18/16 10:30 AM, Rakesh Sharan wrote:
> > > Thanks very much Justin.
> > >
> > > Actually I am minimization a series of configurations from an
> > equilibrated
> > > trajectory of bulk TIP4P/2005 (LINCS used as constraint algorithm). I
> > need
> >
> > So, to be clear, you altered the TIP4P topology to use a system of 3
> > constraints
> > that were held rigid by LINCS, using "constraints = all-bonds" when doing
> > the
> > simulation?  Simply setting LINCS as the constraint method in the .mdp
> > file is
> > insufficient to turn off SETTLE (which is always used unless you tell
> > mdrun not to).
> >
> > > the final energy of the energy minimized structures, however, you can
> see
> > > that depending on the choice of constrained algorithm, for few
> > > configurations, the final energy is different (e. g. for the attached
> > plot
> > > -29146 and -29288 kj/mol). Actually, both are following same
> minimization
> >
> > The list doesn't allow attachments.
> >
> > Re-minimizing a configuration with different algorithms may lead to some
> > differences, I would suspect.  But the internal geometry should be the
> > same, so
> > all that's varying will be LJ and electrostatic terms.  You can check by
> > doing a
> > further decomposition into which term is changing the most.
> >
> > > trajectory, however, one is finishing before other. This is bit
> troubling
> > > as depending on the choice of constraint algorithm average final energy
> > is
> > > different even though initial starting configuration is exactly same. I
> > > rechecked topology files and they look same apart from constraint
> > > specifications.
> > >
> >
> > So let me clarify, because I'm not sure if I follow what you're saying
> > (because
> > here it sounds like you're talking about running different simulations,
> > whereas
> > above it sounds like a very different case).  Which is true:
> >
> > 1. You are doing two simulations from the same starting configuration and
> > are
> > trying to compare the final energy.
> > 2. You are re-minimizing each frame of an existing trajectory and
> comparing
> > energies.
> >
> > #1 really doesn't make sense, as all MD simulations are chaotic, and I'm
> > not
> > sure what #2 would achieve.
> >
> > > I would very much appreciate your view over the plausible origin of
> this
> > > discrepancy. Also, I am wondering whether in both the cases one is
> doing
> > > truly constrained minimization.
> > >
> >
> > If there are no bond or angle energy values, the waters were constrained.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
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