[gmx-users] ffoplsaa.rtp tip4p

[David van der Spoel]

On Tue, 2003-07-01 at 16:53, Kay Gottschalk wrote:
> Hmm, it didn't quite work like that: I extracted the water entries and  
> did the mkyaw stuff - but the output was a bit unexpected: resname was  
> now ??? (which I changed to HOH) and it added a DW and an SW atom at  
> the same coordinates - shouldn't it just add one MW? At least I deleted  
> the SW and renamed the DW to MW, just concatenated the old .gro  
> (without the waters) with the new water.gro file, changed the  
> definition for the water in the topology file and continued pretending  
> that nothing unusual has happened. Now I could at least run the energy  
> minimization. Whether what I did is sensible or not is actually beyond  
> me... Checking visually with VMD shows a nice little dummy next to the  
> oxygen, and that's what we like to see, isn't it? Help would be  
> appreciated.

all set, you could have given an option -nodw to mkyaw, but I think
you've done everything required.  
Simulate on..
> Thanks,
> Kay
> 
> On Tuesday, July 1, 2003, at 03:53 PM, David van der Spoel wrote:
> 
> > On Tue, 2003-07-01 at 14:30, Kay Gottschalk wrote:
> >> Hi there,
> >> did anyone update ffoplsaa.rtp to match tip4p-water?
> >> Thanks,
> > You want to do this differently. It's a bit more complicated.
> > Just generate SPC as usual (e.g. crystal waters). Then you take the
> > waters out of the conf file (e.g. using editconf) and use
> > the program src/contrib/mkyaw to add dummies to the waters. and finally
> > put them back. Don't forget to update the include file for the  
> > topology.
> >
> >
> >> Kay
> >>
> >> _______________________________________________
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> > --  
> > Groeten, David.
> > _______________________________________________________________________ 
> > _
> > Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
> > Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> > phone:	46 18 471 4205		fax: 46 18 511 755
> > spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 
> > +
> > _______________________________________________
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> >
> >
> Dr. Kay-E. Gottschalk
> Department of Biological Chemistry
> Weizmann Institute of Science
> Tel: ++972-8-9343639
> Herzl St. 1
> Rehovot 76100
> Israel
> 
> _______________________________________________
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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