Hi Marc,
Can you please send me (privately) your input files and a script that would
allow me to build the prmtop from the psf using chamber and then also the
run scripts you are using in pmemd.cuda. That way I can take a look at it
and try to figure out what is going on.
I agree it is 'code' error and not user error here. But the problem could be
very subtle.
All the best
Ross
> -----Original Message-----
> From: Marc van der Kamp [mailto:marcvanderkamp.gmail.com]
> Sent: Saturday, April 09, 2011 2:41 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] pmemd.cuda crashes due to "Inconsistent hydrogen
> network"
>
> 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 - 22:00:03 PDT
