[gmx-users] Constraints and Energy Minimization

[Justin Lemkul]

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

-- 
==================================================

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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