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 Is this information outdated or is pmemd.cuda just ignoring lj1264=1?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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--
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 - 05:00:03 PST
