Hi again,
Thanks Ross, Carlos and Scott for your replies.
As I mentioned, I am using CHAMBER to get the prmtop, using a psf/crd of a
fully solvated system. CHAMBER has renamed the TIP3 (CHARMM convention) to
WAT, so all my waters are WAT. I further have 24 sodium ions in the solvent
(named SOD, following CHARMM convention, not Na+).
The SOLVENT_POINTERS in the created prmtop list are:
0 12203 0
So this is presumably where things go wrong, as it should be last solute
residue (428 in my case), total number of molecules (? or total number of
solvent molecules? If the first, then 12203 is correct), first solvent
molecule (429 in my case).
(Or perhaps no molecules should be treated with the special solvent SHAKE to
be more true to CHARMM?)
However, manually changing these values in the prmtop did not change the
problem.
I will try to do more testing on Monday.
BTW, I don't think this is really a user error, but perhaps an 'error' in
CHAMBER?
Many thanks,
Marc
On 9 April 2011 00:09, Scott Le Grand <SLeGrand.nvidia.com> wrote:
> Yes, this is user error that is caught by the CUDA code. The FORTRAN code
> should catch this as well IMO. One or more of your waters is incorrectly
> named and not correctly picked up for the specialized SHAKE algorithm for
> waters. So what I've detected is a hydrogen that is supposedly in a water
> molecule but which has more than one bond attached to it.
>
>
> -----Original Message-----
> From: Marc van der Kamp [mailto:marcvanderkamp.gmail.com]
> Sent: Friday, April 08, 2011 8:07 AM
> To: amber.ambermd.org
> Subject: [AMBER] pmemd.cuda crashes due to "Inconsistent hydrogen network"
>
> Hi all,
>
> I have previously successfully run pmemd.cuda_SPDP using an AMBER force
> field.
> I'm now trying to do the same using the CHARMM force field. After
> converting
> psf/crd using CHAMBER to prmtop/inpcrd, sander.MPI and pmemd.MPI have no
> problems with my system/files. However, when I try to run the same on a
> GPU,
> pmemd.cuda_SPDP crashes with the following message:
> Inconsistent hydrogen network, exiting.
>
> I noticed this error message was introduced (or altered) in the
> comprehensive Bugfix.9 (BTW, all current bugfixes, i.e. up to 12, are
> applied):
>
> if ((my_nonfastwat_bond_dat[j].atm_i == atm_j) ||
> (my_nonfastwat_bond_dat[j].atm_i == atm_j))
>
> {
>
> printf("Inconsistent hydrogen network,
> exiting.\n");
>
> + gpu_shutdown_();
>
> exit(-1);
>
> }
>
> The error occurs right after the number of triangulated waters are reported
> in the output ("Number of triangulated 3-point waters found")
>
> FYI, I'm running on an NVIDIA Tesla M2050.
>
> Any suggestions on how to fix this?
>
> Many thanks in advance,
> Marc
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Received on Sat Apr 09 2011 - 03:00:03 PDT
