[gmx-users] Constraints and Energy Minimization
ericsmoll at gmail.com
Sun Apr 26 21:40:09 CEST 2015
Hello Dr Lemkul,
Thank you for the clarification. To summarize: If I have a bond between two
atoms and one of the atoms has a topology "atom" field that begins with the
letter "H," "constraints=h-bonds" will transform it into a constraint.
I have another question. When specifying this "constrained bond," I have an
equilibrium distance but I do not have a force-constant. Is it irrelevant
what value I choose for the force constant if I apply constraints to that
On Sat, Apr 25, 2015 at 9:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 4/25/15 11:01 PM, Eric Smoll wrote:
>> 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
> By atom name. If the first character is 'H' it is converted to a
> Here are a few lines from ffnonbonded.itp in the oplsaa.ff. The atoms
>> 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
> This is only relevant for specifying, e.g. a bond in [bondtypes] between
> CA_C and HA_C. If I understand your original question right, there are no
> parameters for these bonds, so this really isn't relevant.
>> Similarly, here are a few lines from the topology I have built. Note that
>> 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
>> 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?
> Yes. If a bond is listed between the atoms, it will be converted.
> 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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