[gmx-users] rvdw, rlist and rcoulomb for Amber03

[Justin Lemkul]

On 8/25/13 12:01 AM, Rajat Desikan wrote:
> Hi Justin,
> In a recent post
> (http://gromacs.5086.x6.nabble.com/VDW-Cut-off-vs-Switch-with-CHARMM-force-field-td5010695.html;cid=1377399737789-944)
> you commented that:
>
> "Unless you can demonstrate that your changes in cutoffs do not produce
> artifacts or lead to other inaccuracies using robust test systems, I
> wouldn't recommend any deviations."
>
> I have the habit of reading the original forcefield papers and using their
> parameters directly. In this regard, I use rlist=rvdw=rcoulomb=0.8 nm for
> Amber03 (same parameters are used in the following tutorial:
> http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water_(Pt._2)
> ).
>
> My system is a protein in a water box with counter-ions and 0.1M NaCl. It is
> a NVT simulation at 310 K.
>
> My queries are the following
> 1) Are my parameters appropriate for Amber03?

If they come directly from the primary literature that derived them, yes.

> 2) How would I go about constructing robust test systems to demonstrate the
> validity of my parameters for a protein in a water box? What parameters do I
> measure? Energies? Any structural parameters in particular?
>

This question gets asked a lot, and I have resisted answering it because force 
field parameterization is very complex and a simple email is going to be 
insufficient to answer it.  Long story short, whatever parameters you use should 
reproduce or improve upon whatever the original parametrization method was.  For 
some force fields that may be free energy calculations, for others it may be 
reproducing QM energy or configurations, reproducing water interaction energies, 
etc.  Please do not consider this list exhaustive.

-Justin

-- 
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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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