[gmx-users] ffoplsaa.rtp tip4p

[Kay Gottschalk]

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.
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
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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