[gmx-users] Constraints and Energy Minimization

[Eric Smoll]

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
bond?

Best,
Eric

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
>> 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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