[gmx-users] Constraints and Energy Minimization
jalemkul at vt.edu
Sun Apr 26 05:08:17 CEST 2015
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 detected?
By atom name. If the first character is 'H' it is converted to a constraint.
> 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
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 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?
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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