Hi,
I think that I have properly reordered my PDB file,
but the TI calculation still failed.
Do you think that there are any other possible reasons ?
Sincerely yours,
Ryoichi
2019年9月25日(水) 22:16 Ryoichi Utsumi <u.ryoichi1123.gmail.com>:
>
> Hi, David,
>
> Thank you for your comments. I solved this problem by
> installation of the serial version of pmemd.cuda.
> Thank you for your comments.
> I want to ask you a little bit more on pmemd of Amber16, .
>
> For the preparation of the TI calculations, I saw discussions
> in the amber ML, and then I changed the orders of the atoms
> in my PDB file; i.e., I moved metals in a protein just below
> each subunit (before it, the metals were below all of the
> protein atoms).
>
> Subunit 1
> Metals
> Subunit 2
> Metals
> .
> .
> .
>
> After changing the order of metals in PDB file, the minimization was
> apparently successful, but the TI calculation has still stopped at
> ~58 000 steps with too high DV/DL values.
> So, some illegal descriptions are still left in my molecular topology (?)
> and/or others.
>
> Could I ask how I can identify the inappropriate or illegal orders of
> atoms ? Or, could you tell me fundamental rules to determine
> the order of atoms ?
>
> I would be very happy to hear some ideas/suggestions to solve
> the problems. Thank you in advance,
>
> Sincerely yours,
> Ryoichi
>
> 2019年8月15日(木) 10:33 David Case <david.case.rutgers.edu>:
> >
> > On Sat, Aug 10, 2019, Ryoichi Utsumi wrote:
> > >
> > >I am trying to upgrade the version of CUDA, from 7.5 to 8.0, and to
> > >reinstall pmemd(pmemdGTI).
> >
> > Note that the "pmemdGTI" patch was only a temporary expedient, and development
> > of that has been folded into the main Amber code as of Amber18. So, the
> > "correct" appraoch is to upgrade. Problems with pmemdGTI are unlikely to get
> > a lot of support.
> >
> > However: are you sure that you need pmemd.cuda.MPI? The serial version of
> > pmemd.cuda is (in general) more useful to people.
> >
> > If you do want to get more help here, we would need details of what MPI
> > installation you are using, as well as which CPU compilers.
> >
> > ....regards...dac
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
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Received on Mon Sep 30 2019 - 20:00:02 PDT
