[gmx-users] ffoplsaa.rtp tip4p
kay.gottschalk at weizmann.ac.il
Tue Jul 1 16:54:00 CEST 2003
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
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?
> 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
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
> 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
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
Dr. Kay-E. Gottschalk
Department of Biological Chemistry
Weizmann Institute of Science
Herzl St. 1
More information about the gromacs.org_gmx-users