[gmx-users] question about OPLS-AA force field -required bond constraints

[Michael Shirts]

OPLS-AA was generally derived with Monte Carlo, which means that all
bonds were exactly constrained.  But read the papers!

On Thu, Oct 10, 2013 at 12:27 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 10/10/13 12:17 PM, Martin, Erik W wrote:
>>
>>
>> Hi, I'm new to both Gromacs and OPLS.  I have always used CHARMM or AMBER
>> before so am a bit confused about some idiosyncrasies.
>>
>> When I go to a production run on my system (a protein in a truncated
>> octahedron box of Tip4 water) I have removed all constraints.  When I run
>> grompp, I get an error telling me that a bond between a HG proton and OG
>> oxygen of protein has an oscillation period of 9e-3 ps and is incompatible
>> with my 1 fs time step.  I am used to being able to run a completely
>> unconstrained simulation with a 1 fs time step… so I'm assuming this is a
>> property of OPLS-AA?
>>
>
> No, it's not.  It's a property of the bonds.  Nearly all force fields (if
> not all of them) constrain X-H bonds at minimum, to remove the fastest
> motions in the system and allow for a longer time step.  Using dt on the
> same order as the fastest frequencies leads to instability.  See manual
> section 6.7.
>
>
>> Could someone please let me know what the bond constraint requirements are
>> for OPLS-AA and GROMOS forcefields (I'm going to need to use that next).
>> I
>> can't seem to find this information by searching but imagine its on a
>> website
>> somewhere?
>>
>
> Information like this should be in the primary literature for the parameter
> sets.  I don't know of any sort of database online that tracks such things,
> and moreover there are no absolute rules AFAIK.  I generally follow the
> methods of the paper that derived the parameter set.  Unfortunately,
> sometimes they don't say.  For Gromos96 53A5/53A6, validation simulations
> were carried out with all bonds constrained.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
> ==================================================
>
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