[gmx-users] All atom FF to united atom FF

[Erik Lindahl]

Hi Dallas,

It depends. If the hydrogens lack Lennard-Jones parameters you can  
probably get by with just adding up the charges and masses to form  
united atoms.

If there are LJ parameters on the hydrogens you might need to  
reparameterize things, but it is usually easier for united-atom  
forcefields since there are fewer degrees of freedom. If that is  
complicated I would still try the first approach since the hydrogen  
radii are way smaller than carbons/oxygens.

Normally you optimize for the density and heat of vaporization.

Cheers,

Erik

On Monday, Mar 31, 2003, at 19:03 US/Pacific, Dallas Warren wrote:

> I have found some parameters for ethylene oxide groups which were  
> derived for an all atom force field.  However, with the simulations I  
> am performing with various other components I am using an united atom  
> force field (ffG43a2x with some of my own modifications).  I would  
> like to continue calculations by ignoring the hydrogens attached to  
> the carbon atoms because it significantly reduces the number of atoms  
> in the systems, and therefore increases the calculation speed.
>
> I have a feeling that it is non-trivial to move to an united atom  
> force field and would require re-derivation/determination of the  
> carbon non-bonding parameters to fit the experimental/quantum data so  
> that the hydrogen ion interactions are grouped in with the carbons.   
> Is this the case?  Or can you simple drop out the hydrogen atoms?
>
> Wouldn't be too hard to try out the all and united in that case and  
> see what sort of difference it would make .... will certainly try that  
> if someone else knows better.
>
> Thanks.
>
> Catch ya,
>
>
>
> Dr. Dallas Warren
> Research Fellow
> Department of Pharmaceutical Biology and Pharmacology
> Victorian College of Pharmacy
> Monash University
> 381 Royal Parade
> Parkville VIC 3010
> dallas.warren at vcp.monash.edu.au
> +61 3 9903 9083
>
>
------------------------------------------------------------------------ 
-----
Erik Lindahl, MSc, PhD     <lindahl at stanford.edu>
D109, Fairchild Building
Dept. Structural Biology, Stanford University School of Medicine
Tel. 650-7250754    Fax. 650-7238464

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