Ah then pmemd should be quitting (GPU or CPU) with an error message when lj1264=1 and not just silently running and giving incorrect answers.
> On Jan 31, 2017, at 07:53, Marcelo Andrade Chagas <andrade.mchagas.gmail.com> wrote:
>
> Hi,
>
> Lj 12-6-4 is avaliable for sander, sander.MPI, and not by pmemd or pmemd.MPI
>
> Regards
>
> No dia terça-feira, 31 de janeiro de 2017, Ross Walker <
> ross.rosswalker.co.uk> escreveu:
>
>> Hi Andreas,
>>
>> No, unfortunately GPU code was never written for the 12-6-4 LJ model so it
>> is CPU only I am afraid. However, it's strange that the GPU code would just
>> run with it. At the time 12-6-4 was added to PMEMD a check should have been
>> added to the GPU startup code to quit if 12-6-4 was detected. The authors
>> of the 12-6-4 model should check this.
>>
>> All the best
>> Ross
>>
>>> On Jan 31, 2017, at 04:40, Andreas Tosstorff <
>> andreas.tosstorff.cup.uni-muenchen.de <javascript:;>> wrote:
>>>
>>> Hi all,
>>>
>>> I want to run some REMD simulations with a peptide/Zinc system.
>>>
>>> I wanted to use th 12-6-4 LJ-Type Nonbonded model.
>>>
>>> I generated the parm7 and crd files according to the manual and ran my
>>> first simulation using pmemd.cuda.
>>>
>>> lj1264 is set to 1 and the simulation ran without any errors, however it
>>> did not produce the expected outcome, meaning that Zn2+ would bind to a
>>> HIE residue in its proximity.
>>>
>>> I read in the manual that lj1264 is not supported by pmemd.cuda.
>>>
>>> Is this information outdated or is pmemd.cuda just ignoring lj1264=1?
>>>
>>> Should I rather use 12-6 LJ-Type with pmemd.cuda?
>>>
>>>
>>> Kind regards,
>>>
>>>
>>> Andreas
>>>
>>>
>>> --
>>> M.Sc. Andreas Tosstorff
>>> Lehrstuhl für Pharmazeutische Technologie und Biopharmazie
>>> Department Pharmazie
>>> LMU München
>>> Butenandtstr. 5-13 ( Haus B)
>>> 81377 München
>>> Germany
>>> Tel.: +49 89 2180 77059
>>>
>>>
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>>
>>
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>
>
> --
> Marcelo Andrade Chagas, MSc
> (PhD student)
> Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
> * http://lqcmm.qui.ufmg.br/
> Departamento de Química da Universidade Federal de Minas Gerais - UFMG
> Tel:(31)3409-5776
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Received on Tue Jan 31 2017 - 05:30:04 PST
