[gmx-users] Error while pulling a settled tip4p water molecule

[Jochen Hub]

chris.neale at utoronto.ca wrote:
> I have done a similar thing in the past (without using the pull code), 
> renaming the crystal waters around the protein so that they were 
> easier to track.
>
> I eventually figured out that it was necessary for me to place the 
> waters sequentially in the .top file. e.g:
>
> ; This is OK
> Protein 1
> SOL 999
> XSOL  1
>
> ; This crashed
> SOL 999
> Protein 1
> XSOL  1
>
> I realize that I was getting different errors than you are, but it's 
> worth checking if this fix works for you.
>
> My old post is here 
> http://lists.gromacs.org/pipermail/gmx-users/2006-September/024003.html 
> although it doesn't contain any relevant information other than what I 
> have mentioned above.

Ah thanks. For me it was already fine to replace the settle-line by 3 
constraints:
; [ settles ]
; OW    funct   doh        dhh
; 1       1       0.09572    0.15139
[ constraints ]
; turned settle into normal constraint
1  2  1 0.09572
1  3  1 0.09572
2  3  1 0.15139

Jochen
>
> Chris.
>
> --- original message ---
>
> Berk Hess wrote:
> Hi,
>
> I don't understand why you got this error message.
> Do you have two different types of water molecules with different
> geometries?
>
> In that case Gromacs would give this error message, because
> currently only
> one geometry is supported for settle, so you'll have to replace
> the others
> by 3 normal constraints.
> Ah, all right. I have indeed a separate topology for the water used in 
> the pulling (to be able to give it a different residue name). I have
> replaced the settle by 3 constraints and now everything works fine.
> But if the you make the geometry identical, it should still work with
> settle,
> since then the two settle geometries are identical.
>
> Berk
> Then there is something odd. The two settles are definitely identical
> since I simply copied the tip4p.itp. I also just rechecked with xxdiff,
> the two settle lines are the same.
>
> Jochen
>


-- 
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Dr. Jochen Hub
Molecular Biophysics group
Dept. of Cell & Molecular Biology
Uppsala University. Box 596, 75124 Uppsala, Sweden.
Phone: +46-18-4714451 Fax: +46-18-511755
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