[gmx-users] Position restraints and double precision

[Justin Lemkul]

On 4/14/14, 8:45 AM, Miguel Caro wrote:
> Hi all,
>
> I am trying to do an MD simulation of a small hexagonal box where I need some of
> the atoms to stay fixed. This is because I am mixing ab initio and classical MD
> and some of the atoms in my system should remain within the configuration
> predicted by DFT.
>
> As far as I know, GROMACS only allows energy penalties, rather than true
> position constraints, and so I have to resort to extremely high energy penalties
> for some of the atoms:
>
>     [ position_restraints ]
>     ;  i funct       fcx        fcy        fcz
>         1    1       100000000       100000000       100000000
>         2    1       100000000       100000000       100000000
>     etc...
>
> The above restraints still lead to a small oscillation of the "fixed" atoms.
> These numbers being so large means that the number of significant figures
> allowed for the total energy during the energy minimization is limited to very
> few decimal places using single precision. As a matter of fact, GROMACS
> complains that convergence to machine precision is achieved before the required
> precision.
>
> I guess I have two questions:
>
> 1) Why do I need such huge energy penalties to fix my atoms?
>

Because, as you say above, position restraints don't fix the position of atoms. 
  You can apply a bias to disfavor movement, but it will still move. 
Fortunately, you can actually fix atoms using freezegrps.

> 2) Will the precision issue also affect an MD run or only the EM run? Should I
> reinstall GROMACS in double precision?
>

The precision issue that you're referring to affects EM algorithms; I doubt 
there would be any practical problem during MD.  Most of the truly sensitive 
calculations during MD are actually done in double precision, regardless of the 
chosen output precision.

-Justin

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA 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
http://mackerell.umaryland.edu/~jalemkul

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