Hi Samuel,
You're correct that there shouldn't be a difference in how you use Paramfit
with more or fewer structures.
The problems you're seeing are coming from the operating system and your
script.
The "Killed" message is the out-of-memory (OOM) killer killing Paramfit as
there isn't enough memory available. If you're running on a compute
cluster, you can increase the memory available to the job. If you're
running on your own machine, you can adjust the nice-ness of the process,
use swap, killing other memory-intensive processes, etc.
The "syntax error" message seems to be coming from bash, so I'm guessing
you're using a script to call paramfit and somehow it's trying to execute
the output of Paramfit, which gives syntax errors. If you attach your run
script I can tell you more specifically.
Hope this helps,
Robin
On Fri, Aug 14, 2020 at 2:58 PM Samuel Himes <sam.himes92.gmail.com> wrote:
> Hello Amber Users,
>
> I am attempting to use Paramfit to generate parameters for molecules of
> interest. In my initial trial I was able to run paramfit from start to
> finish with 20 structures. I wanted to repeat the process but this time
> with about 350 structures. This time I can only complete the first step to
> fit K with that many structures. After that I use the following job control
> file.
>
> # Run a fit to energies using the parameters defined earlier
> RUNTYPE=FIT
> COORDINATE_FORMAT=TRAJECTORY
> NSTRUCTURES=364
> K=-292501548281.682251
> PARAMETERS_TO_FIT=LOAD
> PARAMETER_FILE_NAME=prms.in
> FUNC_TO_FIT=SUM_SQUARES_AMBER_STANDARD
> QM_ENERGY_UNITS=HARTREE
>
> # Use the genetic algorithm with the following settings
> ALGORITHM=GENETIC
> OPTIMIZATIONS=50
> MAX_GENERATIONS=10000
> GENERATIONS_TO_CONV=20
> GENERATIONS_TO_SIMPLEX=5
> GENERATIONS_WITHOUT_SIMPLEX=5
> MUTATION_RATE=0.100000
> PARENT_PERCENT=0.250000
> SEARCH_SPACE=-1.000000
> SORT_MDCRDS=OFF
>
> # Output files for later analysis
> WRITE_ENERGY=fit_output_energy.dat
>
> Every time I run it says “Killed” after about 30-40 minutes. Additionally
> it throws these errors.
>
> -bash-4.2$ -350.1297 kcal/mol, Np = 2.0000, Phase = 180.0001 Deg
> bash: -350.1297: command not found...
> -bash-4.2$ (n -c3-nh-ce)*Kp = 351.1492 kcal/mol, Np = 2.0000,
> Phase = 0.0000 Deg
> -bash: syntax error near unexpected token `*Kp'
> -bash-4.2$ (n -c3-nh-c3)*Kp = -23.1425 kcal/mol, Np = 2.0000,
> Phase = 0.0000 Deg
> -bash: syntax error near unexpected token `*Kp'
> -bash-4.2$ (n -c -c3-nh)*Kp = 93.5440 kcal/mol, Np = 2.0000,
> Phase = 180.0001 Deg
> -bash: syntax error near unexpected token `*Kp'
> -bash-4.2$ (n -c -c3-c3)*Kp = -73.0671 kcal/mol, Np = 2.0000,
> Phase = 180.0001 Deg
> -bash: syntax error near unexpected token `*Kp'
> -bash-4.2$ (n -c -c3-c3)*Kp = 23.1595 kcal/mol, Np = 4.0000,
> Phase = 180.0001 Deg
> -bash: syntax error near unexpected token `*Kp'
> -bash-4.2$ (nh-ce-ce-c2)*Kp = -219.8412 kcal/mol, Np = 2.0000,
> Phase = 180.0001 Deg
> -bash: syntax error near unexpected token `*Kp'
> -bash-4.2$ (nh-c3-n -c3)*Kp = 146.5671 kcal/mol, Np = 2.0000,
> Phase = 0.0000 Deg
> -bash: syntax error near unexpected token `*Kp'
> -bash-4.2$ (nh-c3-n -c )*Kp = 60.3180 kcal/mol, Np = 2.0000,
> Phase = 0.0000 Deg
> -bash: syntax error near unexpected token `*Kp'
> -bash-4.2$ (nh-c3-c -o )*Kp = -14.6946 kcal/mol, Np = 2.0000,
> Phase = 180.0001 Deg
> -bash: syntax error near unexpected token `*Kp'
> -bash-4.2$ (nh-c3-c3-ca)*Kp = 896.3533 kcal/mol, Np = 3.0000,
> Phase = 0.0000 Deg
> -bash: syntax error near unexpected token `*Kp'
> -bash-4.2$ (c3-c3-nh-ce)*Kp = 843.2682 kcal/mol, Np = 2.0000,
> Phase = 0.0000 Deg
> -bash: syntax error near unexpected token `*Kp'
> -bash-4.2$ (c3-c3-n -c3)*Kp = -24.0452 kcal/mol, Np = 2.0000,
> Phase = 0.0000 Deg
> -bash: syntax error near unexpected token `*Kp'
> -bash-4.2$ (c3-c3-n -c )*Kp = 77.9657 kcal/mol, Np = 1.0000,
> Phase = 180.0001 Deg
> -bash: syntax error near unexpected token `*Kp'
> -bash-4.2$ (c3-c3-n -c )*Kp = 28.4979 kcal/mol, Np = 3.0000,
> Phase = 0.0000 Deg
> -bash: syntax error near unexpected token `*Kp'
> -bash-4.2$ (c3-c3-n -c )*Kp = 32.4247 kcal/mol, Np = 4.
> -bash: syntax error near unexpected token `*Kp’
>
> The parameters that I’m setting to fit about 64 dihedral angles using the
> KP setting.
> Has anyone encountered a problem similar to this? Is it that I am simply
> using too many structures, or is there a different problem? If the problem
> has to do with the amount of structures how many structures are usually
> necessary to create good parameters?
>
> Thanks in advance for the help.
> -Sam
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Received on Fri Aug 14 2020 - 15:30:03 PDT
