[gmx-users] Constraints and Energy Minimization

Eric Smoll ericsmoll at gmail.com
Sun Apr 26 05:01:35 CEST 2015

Hello Dr Lemkul,

Thank you for the rapid response. It is much appreciated.

On the subject of specifying constraints, how does the mdp keyword-value
pair: "constraints=h-bonds" work?  How are the bonds with hydrogen detected?

Here are a few lines from ffnonbonded.itp in the oplsaa.ff. The atoms shown
are for custom hydrogen additions to the opls forcefield. Note that the
"bond_type" field begins with the element letter (in this case, "C" and
"H") and has a suffix.

[ atomtypes ]

; full atom descriptions are available in ffoplsaa.atp
; name  bond_type    mass    charge   ptype          sigma      epsilon
  opls_972    CA_C   6      12.01100    -0.130       A    3.55000e-01
 2.92880e-01  ;SIG
  opls_973    HA_C   1       1.00800     0.210       A    2.42000e-01
 1.25520e-01  ;SIG

Similarly, here are a few lines from the topology I have built. Note that I
prefer to have the "atom" field list the chemical element (again "C" and
"H") followed by a numerical suffix. In general my ffnonbonded "bond_type"
field and the topology "atom" field do not match and are never just labeled
with the element name.

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB
   chargeB      massB
  1096   opls_972     42    CCC     C5    332      -0.13     12.011   ;
qtot -13.07
  1097   opls_973     42    CCC     H6    332       0.21      1.008   ;
qtot -12.86

Will "constraints=h-bonds" correctly identify C-H bonds in my system
without manually adding to the topology?


On Sat, Apr 25, 2015 at 8:27 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

> On 4/25/15 10:25 PM, Eric Smoll wrote:
>> Hello Gromacs Users,
>> I am studying a forcefield where certain bond force constants were not
>> specified because the associated bond lengths were "constrained." What do
>> I
>> need to do to run a simulation that is consistent with the way this
>> forcefield was designed? Will LINCS constraints satisfy this requirement
>> faithfully?
> Specify [constraints] in the topology with the correct length.  LINCS will
> satisfy it; that's what it was designed to do.
>  In a molecular dynamics workflow, when are constraints best introduced?
>> For
>> example, should constraints be used during energy minimization?
> Sounds like your force field requires it, so there's really no question.
> In general, I say if you're going to run the MD with constraints, you need
> to minimize with constraints.  All too often I have seen bad geometries
> come from unconstrained EM, which upon starting MD with constraints, cause
> failure.  An initial EM without constraints may be needed if the initial
> geometry is really bad, but a subsequent constrained minimization is a good
> idea in that case.
> -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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