Ok.
This is in Amber14?
Thanks.
No dia terça-feira, 31 de janeiro de 2017, Andreas Tosstorff <
andreas.tosstorff.cup.uni-muenchen.de> escreveu:
> There is at least one publication stating that it used 12-6-4 with pmemd:
>
> DOI: 10.1021/acs.jctc.6b00173
>
>
> On 01/31/2017 02:11 PM, Qinghua Liao wrote:
> > It currently only supports sander and pmemd
> > (both the serial and MPI versions) but not pmemd.cuda.
> >
> > copied from the manual (page 321)
> >
> > On 01/31/2017 01:53 PM, Marcelo Andrade Chagas 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 <javascript:;>> 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:;> <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 Is this information outdated or is pmemd.cuda just ignoring lj1264=1?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
> >>>>
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org <javascript:;> <javascript:;>
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org <javascript:;> <javascript:;>
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org <javascript:;>
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org <javascript:;>
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 31 2017 - 06:00:03 PST
