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

[chris.neale at utoronto.ca]

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.

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