[gmx-users] Is the new version of Gromacs going to be able to do implicit water md?

Erik Lindahl lindahl at cbr.su.se
Fri Oct 10 06:00:23 CEST 2008


Not 4.0, but it's in the pipeline for 4.1.

The issue is not doing it, but doing it clearly faster than explicit  
water MD, since water interactions are extremely optimized in Gromacs!



On Oct 9, 2008, at 2:38 PM, Arthur Roberts wrote:

> Hi, all,
> I know this question might seem almost heretical because I am aware  
> of the issues with implicit water md.  I actually prefer explicit  
> waters because I think it more realistically represents the water  
> environment.  However,  the problem with explicit waters is that the  
> calculation is time consuming.  I am collaborating with industry and  
> we need a relatively rapid way to do MD that doesn't require a  
> computer cluster.  Therefore, I was wondering if Gromacs 4.0 will be  
> able to do implicit water calculations that will significantly speed  
> up the calculation?  I know the previous version didn't.  Your input  
> is much appreciated.
> Best wishes,
> Art Roberts
> University of Washington
> Seattle, WA
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