Thanks for the feedback.
It's good to see that you learn from incorrect answers!
When I tested the nonbonded model using 12-6-4 LJ for my system
with AMBER14 only worked sander and sander.MPI and from what I had seen
had not yet been implemented for pmemd.
I will test later for curiosity if with AMBER16 it works then same.
Our group recently acquired new license due to new machines
that we acquired with GPUs not being compatible with AMBER14 and not having
updates for that, as far as I know.
However, the nonbound model did not work for my metaloprotine system with
two transition metal ions
on the active site and I started to use the attached model with MCPB.py
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
2017-01-31 12:11 GMT-02:00 Christina Bergonzo <cbergonzo.gmail.com>:
> 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
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> > > >>>> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Jan 31 2017 - 07:00:04 PST
