Re: [AMBER] Installaiton of pmemd for Amber16

From: Ryoichi Utsumi <>
Date: Wed, 25 Sep 2019 22:16:40 +0900

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
Subunit 2

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,

2019年8月15日(木) 10:33 David Case <>:
> 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 mailing list
Received on Wed Sep 25 2019 - 06:30:04 PDT
Custom Search