I support unlimited solvent molecules. I just need to improve the
definition.of solvent for these systems. Factor IX is in water. And this
issue is only for NTP.
On Aug 9, 2011 11:15 AM, "Ismail, Mohd F." <farid.ou.edu> wrote:
> I don't get the hard cap part.
>
> For my system I have (right now) 64,000 atoms, and the NPT (npt=1, ntb=2)
ensemble fails and spits out that error. The NVT (ntb=1, npt=0) works fine.
>
> But I also ran the FactorIX_Production_NPT (with 90,000+ atoms) and
FactorIX_Production_NVT and both ran fine.
>
> Or are you saying it's the molecules (residue) number? Then I have 4000
molecules. I'm not sure about the FactorIX benchmark molecules.
>
> Regards,
> Farid Ismail
>
> ________________________________________
> From: Scott Le Grand [varelse2005.gmail.com]
> Sent: Tuesday, August 09, 2011 12:28 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Failure kReduceSoluteCOM with GPU
>
> The problem they're hitting here is that C1060 is hard-capped to 460
solute
> molecules and C20xx is capped to 1535.
>
> I've fixed that but it's still in testing. That said, what would be useful
> here is for you guys to tell me the maximum number of atoms you'll
generally
> use in these alternate solvent molecules so I can optimize performance for
> these down the road.
>
> Scott
>
>
>
> On Tue, Aug 9, 2011 at 9:15 AM, Jason Swails <jason.swails.gmail.com>
wrote:
>
>> On Tue, Aug 9, 2011 at 10:47 AM, Ismail, Mohd F. <farid.ou.edu> wrote:
>>
>> > I have also stumbled into this error. My system is a 64,000 atom system
>> > made of 4000 dimethoxy ethane molecule.
>> >
>> > My system is a dual opteron with GTX 590, cuda 3.2, Nvidia driver
280.16,
>> > and gfortran.
>> >
>> > If I run the system with NPT ensembles, it fails. But if I run with NVT
>> > ensemble, it works fine. I never test it with NVE calculation. Both
>> system
>> > works when run on CPU. The weird thing is the benchmark system
>> > Factorial....NPT runs fine. The only different I found is the benchmark
>> > system uses the old parameter file, whereas the my system run the new
>> > parameter file (the part in the mdout that says "New format PARM file
>> being
>> > parsed.")
>> >
>> > I assume the old format PARM is for AmberTools <1.5, no?
>> >
>>
>> No. Old parm format is actually < Amber 7, which is pretty severely
>> outdated at this point (not sure exactly when it was released -- maybe
>> ~2004
>> or so?).
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Tue Aug 09 2011 - 11:30:04 PDT
