In the cited publication, I used Amber14* pmemd.MPI with the 12-6-4 LJ
model.
*The version of Amber14 I used contained all updates and bugfixes through
March 2016, so make sure your code is up to date for the implementation to
work!
You can run a quick test where you modify the C4 section of the parmtop to
some outrageous numbers to make sure pmemd.MPI is using it.
Also remember to set lj1264=1 in your input file.
-Christina
On Tue, Jan 31, 2017 at 8:36 AM, Marcelo Andrade Chagas <
andrade.mchagas.gmail.com> wrote:
> 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
> > >>>
> > >
> > > _______________________________________________
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> > > 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
>
--
--------------------------------------------------------------
Christina Bergonzo
Research Chemist
NIST/IBBR NRC Postdoctoral Researcher
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Received on Tue Jan 31 2017 - 06:30:02 PST
