[gmx-users] Amber Force field in Gromacs - implicit solvent

Erik Lindahl lindahl at stanford.edu
Sun Oct 20 07:28:04 CEST 2002


>>Finally I would like to know if there is any project to incorporate some kind 
>>of implicit solvent model in gromacs.
>Also the Pande group together with Erik Lindahl have done this. Don't
>know about the status of this.
We're currently testing a couple of different setups. There are for 
example two different ways of calculating the GBSA interactions, and we 
have one fast and one accurate way of calculating the surface and 
surface derivatives. We need to test things a bit more and see which one 
we should implement in Gromacs....

Still - GBSA will probably NOT be significantly faster for dynamics 
simulations, mainly because the interactions are by definition much more 
complicated to calculate. The main advantage is probably that it is 
easier to energy minimize structures without the water (it's easier for 
the protein to move that way).



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