Hi, Stefan
You should be able to use &pmd when you update to the latest Amber16, can
you
send me your input file so I can test to find what is the problem.
You can send to my email fpan3.ncsu.edu
Feng
On Tue, May 1, 2018 at 12:04 PM, Lenz, Stefan <stefan.lenz.uleth.ca> wrote:
> Dear AMBER developers:
>
> I am trying to use the &pmd module with pmemd.cuda (or pmemd.cuda.MPI) on
> AMBER16. I have successfully ran my input file using pmemd, however, I get
> errors when I try to use the GPU code.
>
> The version of AMBER16 I am using has the patches up to update.11 applied.
> According to the manual (Amber17.pdf) what I am trying to do should be
> possible: "*From Amber16, we implement these modules from SANDER to PMEMD
> and the modules are GPU compatible." *pg. 441.
>
> When I run my input file, I get the error: *invalid reference to variable
> in NAMELIST input, unit 5, file user_inputfile.in
> <http://user_inputfile.in> line 14, position 7.*
>
> That error points me to my input file:
>
> user_inputfile.in
> title
> &cntrl
> ...
> ntpr = 2500, ntwx = 5000, ntwr = -125000,
> infe=1 *[line 14]*
> /
> &pmd
> output_file = 'temp_info.dat'
> output_freq = 1
> cv_file = 'cv.in' [*from AMBER manual pg. 447]*
> /
>
> I get the same error using pmemd.cuda, pmemd.cuda.MPI, and pmemd.MPI, but
> my input file runs fine using pmemd.
>
> So pmemd.cuda is having trouble parsing infe=1. My question is if &pmd
> usage is implemented in pmemd.cuda, and if so whether someone can help me
> troubleshoot my input file. If &pmd usage is not implemented in
> pmemd.cuda(.MPI) (AMBER16), I was wondering if it is implemented in
> pmemd.cuda(.MPI) (AMBER18).
>
> Any help would be greatly appreciated,
>
> Stefan
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>
--
Feng Pan
Ph.D.
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Wed May 02 2018 - 14:00:02 PDT
