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

[Mark Abraham]

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
>
> ==================================================
> --
> 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-request at gromacs.org.
>