[gmx-users] Constraints and Energy Minimization
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
opls_973 HA_C 1 1.00800 0.210 A 2.42000e-01
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
1096 opls_972 42 CCC C5 332 -0.13 12.011 ;
1097 opls_973 42 CCC H6 332 0.21 1.008 ;
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
>> need to do to run a simulation that is consistent with the way this
>> forcefield was designed? Will LINCS constraints satisfy this requirement
> 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?
>> 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 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
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