[gmx-users] Force Fields and Electrostatics

Dallas Warren dallas.warren at vcp.monash.edu.au
Wed Mar 31 03:27:02 CEST 2004

Just wondering on a couple of things to do with force fields and the 
electrostatics used in them.

Force fields are developed with particular electrostatics in mind, right? 
i.e. cut-off of a certain length or PME etc.

What happens then if you then use something different?  Does the ff take 
into "account" the irregularities (eg with cut-off you get concentration of 
oppositely charged ions at the cut-off distance when looking at the RDF) 
that occur and therefore if you use a different electrostatic treatment 
things start to breakdown?  In other words, do you just stick to what is 
defined by the ff to be used?

I have run three simulations of the same system with different treatment of 
electrostatics.  This is been done using the G43a2 force field.  The 
different conditions I have used are listed below.  The behaviour of all of 
them is different to each other.
         Cut-off 1.5 nm
         Cut-off 2.0 nm

I have noted that Marrink + Mark (BioChem 41(17) 5375 2002) used a similar 
system with 1.5 nm, tested out 1.8 nm and saw not overall difference, using 
Gromos96.  So they settled at 1.5 nm being OK to use.

I was thinking that may be that the ff is developed on simpler systems such 
that the important interactions that produce the properties things are 
adjusted for are under these cut off distances.  So when electrostatic 
interactions that are over a similar distance to the cut-off, or a bit 
larger, things can be adversely effected and behave in an unusual manner.

This is something that probably goes to the heart of the black art of force 
fields ;-)

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
When the only tool you own is a hammer, every problem begins to resemble a nail.

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