[gmx-users] Re: grompp warnings/errors I haven't seen before

[David Mobley]

OK, I seem to have traced at least the latter problems back to
something new in gromacs 3.3.2 relative to 3.3.1, in that my system
works fine in 3.3.1 but not in 3.3.2. Is there something new with
handling of constraints or settles for water in 3.3.2 relative to
3.3.1?

I will try submitting a bugzilla with an example input file, I think.
It's possible the problem is on my end somewhere, but as far as I can
tell I'm not doing anything I'm not supposed to...

Thanks,
David


On Jan 3, 2008 2:33 PM, David Mobley <dmobley at gmail.com> wrote:
> All,
>
> I'm trying to simulate a peptide/water/cosolvent mix in gromacs
> (3.3.2). I've set up a topology and coordinates and everything seems
> fine until I run grompp, at which point I get
>
> WARNING 1 [file "solvated.top", line 17]:
>   Overriding atomtype HO
> WARNING 2 [file "solvated.top", line 22]:
>   Overriding atomtype OH
> WARNING 3 [file "solvated.top", line 26]:
>   Overriding atomtype H1
> Generated 210 of the 210 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 210 of the 210 1-4 parameter combinations
> Excluding 3 bonded neighbours for solute 1
> turning H bonds into constraints...
> Excluding 1 bonded neighbours for SOL 4816
> turning H bonds into constraints...
> Excluding 3 bonded neighbours for TFE 805
> turning H bonds into constraints...
> processing coordinates...
> double-checking input for internal consistency...
> renumbering atomtypes...
> converting bonded parameters...
> #      BONDS:   4234
> #     ANGLES:   11205
> #     RBDIHS:   10605
> #       LJ14:   10714
> #     CONSTR:   2615
> #     SETTLE:   4816
> Walking down the molecule graph to make shake-blocks
> Double sids (903, 904) for atom 22086
> Double sids (903, 904) for atom 22087
> Double sids (903, 904) for atom 22088
> Double sids (903, 904) for atom 22089
> Double sids (903, 904) for atom 22090
> Double sids (903, 904) for atom 22091
> Double sids (903, 904) for atom 22092
> Assertion failed for "n == natoms" in file splitter.c, line 668
> dump core ? (y/n):n
>
> I've never seen this stuff before. First off, I don't understand the
> warnings -- what's overriding those atom types? I don't see anything
> wrong with them or anythign that should override them.
>
> Second, what does the business about "Double sids" and "shake blocks"
> mean? Clearly I've got something wrong in my topology or in the
> relationship between my topology and gro file, but this is not at all
> transparent.
>
> I'll poke around in the source and see if I can figure out what's
> going on but I thought I might be able to expedite things by an e-mail
> to the list.
>
> Thanks,
> David Mobley
> http://www.dillgroup.ucsf.edu/~dmobley
>