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Backmapping with martini 2
- nanogod
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2 years 7 months ago #9116
by nanogod
Backmapping with martini 2 was created by nanogod
Hi,
I am trying to backmap a protein with initram.sh. After modifying the program for gromacs2021 i got it to work with the aquaporin tutorial. However, it does not work with my own protein.
I run:
./initram-v5.sh -f system_md.gro -o aa_charmm.gro -p topol.top -to gromos54a7
and get:
Checking dependencies:
backward.py ... Missing dependency: backward.py
I guess i am missing some command for backwards.py but I have no idea what :) Anyone have a suggestion?
Br Morten
I am trying to backmap a protein with initram.sh. After modifying the program for gromacs2021 i got it to work with the aquaporin tutorial. However, it does not work with my own protein.
I run:
./initram-v5.sh -f system_md.gro -o aa_charmm.gro -p topol.top -to gromos54a7
and get:
Checking dependencies:
backward.py ... Missing dependency: backward.py
I guess i am missing some command for backwards.py but I have no idea what :) Anyone have a suggestion?
Br Morten
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- riccardo
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2 years 7 months ago #9117
by riccardo
Replied by riccardo on topic Backmapping with martini 2
This usually means that backward.py is not in the same folder where initram is. So initram cannot find backward.py
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- nanogod
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2 years 7 months ago #9130
by nanogod
Replied by nanogod on topic Backmapping with martini 2
Hi Riccardo, thanks for your reply. unfortunately that's not the case :(
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- nanogod
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2 years 7 months ago - 2 years 7 months ago #9131
by nanogod
Replied by nanogod on topic Backmapping with martini 2
turns out i had a space in my folder and the script couldnt locate backwards.py since it did not accept the space in the directory :) sorry for the trouble
Br Morten
Br Morten
Last edit: 2 years 7 months ago by nanogod.
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- riccardo
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2 years 7 months ago #9132
by riccardo
Replied by riccardo on topic Backmapping with martini 2
Great to hear it's fixed. Thanks for following up.
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- nanogod
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2 years 7 months ago #9142
by nanogod
Replied by nanogod on topic Backmapping with martini 2
now I am really sorry for the incontinence :) I use to run this script with some small modification a couple of years ago, however that must be a long time ago :)
Now I get an error after second minimization run and 2-EM.gro isnt written:
gmx mdrun -deffnm 2-EM -v -nt 0
Reading file 2-EM.tpr, VERSION 2021.2 (single precision)
Multiple energy groups is not implemented for GPUs, falling back to the CPU. For better performance, run on the GPU without energy groups and then do gmx mdrun -rerun option on the trajectory with an energy group .tpr file.
Using 1 MPI thread
Using 12 OpenMP threads
Steepest Descents:
Tolerance (Fmax) = 1.00000e+01
Number of steps = 500
./initram-v5.sh: line 330: 5052 Segmentation fault (core dumped) $M
Now I get an error after second minimization run and 2-EM.gro isnt written:
gmx mdrun -deffnm 2-EM -v -nt 0
Reading file 2-EM.tpr, VERSION 2021.2 (single precision)
Multiple energy groups is not implemented for GPUs, falling back to the CPU. For better performance, run on the GPU without energy groups and then do gmx mdrun -rerun option on the trajectory with an energy group .tpr file.
Using 1 MPI thread
Using 12 OpenMP threads
Steepest Descents:
Tolerance (Fmax) = 1.00000e+01
Number of steps = 500
./initram-v5.sh: line 330: 5052 Segmentation fault (core dumped) $M
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