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

[Rakesh Sharan]

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
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
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.

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.

Best,
Rakesh

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


On Thu, Apr 14, 2016 at 1:07 PM, Rakesh Sharan <rs11chembhu at gmail.com>
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 have
> attached here a minimization trajectory of a configuration using SETTLE and
> LINCS.
>
> I need 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). 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.
>
> 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.
>
> Best,
> Rakesh
>
> ----------------------------------------------------
> Rakesh S. Singh, Ph.D.
> Postdoctoral Research Associate,
> Department of Chemical & Biological Engineering,
> Princeton University,
> Princeton, NJ 08544 (US).
>
>
> On Tue, Apr 12, 2016 at 8:25 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 4/11/16 4:08 PM, Rakesh Sharan wrote:
>>
>>> Hi all,
>>>
>>> I am getting significantly different final energy during energy
>>>
>>
>> How large is the difference?  If it is dramatic, then your coordinates
>> should also be quite different and visualization should provide some
>> clues.  But given that the water molecules are rigid, the only differences
>> will be in nonbonded terms, which means a different configuration.  There's
>> no guarantee that two constraint algorithms will produce identical
>> outcomes, though I would expect them to be close if set up properly.
>>
>> minimization of a box of bulk TIP4P/2005 water using SETTLE and LINCS as
>>> constraint algorithms. I do not know which is more reliable in the sense
>>> that which one is giving correct converged configurations starting from
>>> the
>>> same initial configuration.
>>>
>>> I would highly appreciate your comments/suggestions over this
>>> discrepancy.
>>>
>>> The mdp file that I am using is following:
>>>
>>>
>> The .mdp file is not particularly relevant, as using LINCS vs. SETTLE
>> will have to be done with changes to the topology file.  If you're getting
>> big differences in outcomes, probably whatever modifications you did there
>> are incorrect.
>>
>> -Justin
>>
>>
>> integrator              = steep         ; steepest descents energy
>>> minimization
>>> nsteps                  = 10000          ; maximum number of steps to
>>> integrate
>>>
>>> emtol                   = 1.0          ; [kJ/mol/nm] minimization is
>>> converged when max force is < emtol
>>> emstep                  = 0.01          ; [nm] initial step-size
>>>
>>> nstxtcout               = 10            ; [steps] freq to write to
>>> coordinate file
>>> nstlog                  = 10            ; [steps] freq to write energies
>>> to
>>> log file
>>> nstenergy               = 10            ; [steps] freq to write energies
>>> to
>>> energy file
>>> xtc_grps                = System        ; coordinate group(s) to write to
>>> disk
>>> energygrps              = System        ; group(s) to write to energy
>>> file
>>>
>>> nstlist                 = 1             ; [steps] freq to update neighbor
>>> list
>>> ns_type                 = grid          ; method of updating neighbor
>>> list
>>> pbc                     = xyz           ; periodic boundary conditions in
>>> all directions
>>> rlist                   = 0.95           ; [nm] cut-off distance for the
>>> short-range neighbor list
>>>
>>> rcoulomb                = 0.95          ; [nm] distance for Coulomb
>>> cut-off
>>>
>>> vdw-type                = cut-off       ; twin-range cut-off with rlist
>>> where rvdw >= rlist
>>> rvdw                    = 0.95          ; [nm] distance for LJ cut-off
>>> DispCorr                = Ener          ; apply long range dispersion
>>> corrections for energy
>>>
>>> ;constraints            = none
>>> coulombtype             = PME           ; Particle-Mesh Ewald
>>> electrostatics
>>> pme_order               = 4             ; interpolation order for PME, 4
>>> =
>>> cubic
>>> fourierspacing          = 0.12
>>>
>>> Thanks,
>>>
>>> Best.
>>> Rakesh
>>>
>>> ----------------------------------------------------
>>> Rakesh S. Singh, Ph.D.
>>> Postdoctoral Research Associate,
>>> Department of Chemical & Biological Engineering,
>>> Princeton University,
>>> Princeton, NJ 08544 (US).
>>>
>>>
>> --
>> ==================================================
>>
>> 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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