Maryam
Are you trying to use GEM ?
If not, then you must use pmemd, not gem.pmemd
If pmemd is not in your bin directory, then that is your problem. Either
it did not get compiled at all, or it tried and did not succeed.
Focus on that first, how to get pmemd compiled (or pmemd.cuda if you are
using GPU)
Adrian
On 8/3/23 12:55 PM, Maryam Foroozmehr via AMBER wrote:
> [External Email]
>
> To Whom It May Concern:
>
> It is very appreciated letting me know how to debug the below problem.
> Thank you.
>
> Simple simulation of Alanine dipeptide:
> *Part 19. Run the production MD of alanine dipeptide with pmemd:*
>
> Question: There is no "pmemd" in the bin file, instead there is
> "gem.pmemd". While running it there is the below error:
>
> ERROR: SHAKE (ntc != 1) may not be used with Amoeba or GEM!
>
> *- By considering the error, I made these changes: ntc=1,ntf=1, but then I
> got the below error:*
> *Command:* amber22_src/AmberTools/src/gem.pmemd/src/inpcrd_dat.F90 (unit =
> 9, file = '02_Heat.ncrst')
> Fortran runtime error: Bad value during floating point read
>
> Error termination. Backtrace:
> #0 0x7f3684ffd960 in ???
> #1 0x7f3684ffe4d9 in ???
> #2 0x7f368524faba in ???
> #3 0x7f36852536b9 in ???
> #4 0x7f3685254e55 in ???
> #5 0x559ec62a84f3 in __inpcrd_dat_mod_MOD_init_old_type_inpcrd_dat
> #6 0x559ec62a9d8f in __master_setup_mod_MOD_master_setup
> #7 0x559ec62d646f in MAIN__
> #8 0x559ec61e858e in main
> ^C
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--
Dr. Adrian E. Roitberg
V.T. and Louise Jackson Professor in Chemistry
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Thu Aug 03 2023 - 10:30:02 PDT
