Home >
Community >
Why does the error ccurs while running run_inflategro.sh in gromacs?
Upvote
28
Downvote
+ Running
+ Gromacs
+ Filing
+ Command line
Posted by
Naj Khan
Why does the error ccurs while running run_inflategro.sh in gromacs?
Firstly check whether the .tpr file is in your working directory or not. If it's not there, obviously the .gro file will also not be generated and check your bash script as well.
Firstly check whether the .tpr file is in your working directory or not. If it's not there, obviously the .gro file will also not be generated and check your bash script as well.
didn't work and didn't generate the tpr file. Then, given that you didn't minimize, there is no .gro file and therefore also the trjconv command fails followed by a mv failure because the trjconv step failed. Then the cycle goes on for ${curr}=2 and it exits because the previous step hasn't completed correctly.
The problem is why the grompp passage failed. You should run line by line to debug and find out the exact problem.
didn't work and didn't generate the tpr file. Then, given that you didn't minimize, there is no .gro file and therefore also the trjconv command fails followed by a mv failure because the trjconv step failed. Then the cycle goes on for ${curr}=2 and it exits because the previous step hasn't completed correctly.
The problem is why the grompp passage failed. You should run line by line to debug and find out the exact problem.
Nicola Piasentin and Sutanu Mukhopadhyay I've my system_shrink1.tpr file in my working directory and while running the command gmx mdrun -deffnm system_shrink1_em for getting system_shrink1_em.gro it throws an error stating: segmentation fault (core dumped) this is the same error while running the bash script reason being it does not generate the .gro file. Can anyone help me solving this segmentation fault error?
Nicola Piasentin and Sutanu Mukhopadhyay I've my system_shrink1.tpr file in my working directory and while running the command gmx mdrun -deffnm system_shrink1_em for getting system_shrink1_em.gro it throws an error stating: segmentation fault (core dumped) this is the same error while running the bash script reason being it does not generate the .gro file. Can anyone help me solving this segmentation fault error?
Firstly check whether the .tpr file is in your working directory or not. If it's not there, obviously the .gro file will also not be generated and check your bash script as well.
#!/bin/bash
gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p topol.top -r system_inflated.gro -o system_inflated_em.tpr
gmx mdrun -deffnm system_inflated_em
gmx trjconv -s system_inflated_em.tpr -f system_inflated_em.gro -o tmp.gro -pbc mol mv tmp.gro system_inflated_em.gro
Firstly check whether the .tpr file is in your working directory or not. If it's not there, obviously the .gro file will also not be generated and check your bash script as well.
#!/bin/bash
gmx grompp -f minim_inflategro.mdp -c system_inflated.gro -p topol.top -r system_inflated.gro -o system_inflated_em.tpr
gmx mdrun -deffnm system_inflated_em
gmx trjconv -s system_inflated_em.tpr -f system_inflated_em.gro -o tmp.gro -pbc molmv tmp.gro system_inflated_em.gro
More
VOTE
Sutanu Mukhopadhyay It is not generating system_shrink1_em.gro
Sutanu Mukhopadhyay It is not generating system_shrink1_em.gro
More
VOTE
The errors is most likely due to this line failing at the first iteration, that is for ${curr}=1
gmx mdrun -deffnm system_shrink${curr}_em
In particular the error is telling you that system_shrink1_em.tpr is not present in your directory, which means that the previous grompp command
gmx grompp -f minim_inflategro.mdp -c system_shrink1.gro -r system_shrink1.gro -p topol.top -o system_shrink1_em.tpr
didn't work and didn't generate the tpr file. Then, given that you didn't minimize, there is no .gro file and therefore also the trjconv command fails followed by a mv failure because the trjconv step failed. Then the cycle goes on for ${curr}=2 and it exits because the previous step hasn't completed correctly.
The problem is why the grompp passage failed. You should run line by line to debug and find out the exact problem.
The errors is most likely due to this line failing at the first iteration, that is for ${curr}=1
gmx mdrun -deffnm system_shrink${curr}_em
In particular the error is telling you that system_shrink1_em.tpr is not present in your directory, which means that the previous grompp command
gmx grompp -f minim_inflategro.mdp -c system_shrink1.gro -r system_shrink1.gro -p topol.top -o system_shrink1_em.tpr
didn't work and didn't generate the tpr file. Then, given that you didn't minimize, there is no .gro file and therefore also the trjconv command fails followed by a mv failure because the trjconv step failed. Then the cycle goes on for ${curr}=2 and it exits because the previous step hasn't completed correctly.
The problem is why the grompp passage failed. You should run line by line to debug and find out the exact problem.
More
VOTE
Both the files ('system_shrink1_em.tpr', 'system_shrink1_em.gro') must be in your working directory.
Both the files ('system_shrink1_em.tpr', 'system_shrink1_em.gro') must be in your working directory.
More
VOTE
Nicola Piasentin and Sutanu Mukhopadhyay
I've my system_shrink1.tpr file in my working directory and while running the command
gmx mdrun -deffnm system_shrink1_em
for getting system_shrink1_em.gro it throws an error stating:
segmentation fault (core dumped)
this is the same error while running the bash script reason being it does not generate the .gro file.
Can anyone help me solving this segmentation fault error?
Nicola Piasentin and Sutanu Mukhopadhyay
I've my system_shrink1.tpr file in my working directory and while running the command
gmx mdrun -deffnm system_shrink1_em
for getting system_shrink1_em.gro it throws an error stating:
segmentation fault (core dumped)
this is the same error while running the bash script reason being it does not generate the .gro file.
Can anyone help me solving this segmentation fault error?
More
VOTE