- Posts: 14
problem encounterd when I used cg_bonds.tcl
- Jinyoung
-
Topic Author
- Offline
- Fresh Boarder
Less
More
2 years 7 months ago - 2 years 7 months ago #9108
by Jinyoung
problem encounterd when I used cg_bonds.tcl was created by Jinyoung
Hi,
I tried to visualize the MARTINI force field system with VMD by using cg_bonds.tcl
When I used cg_bonds.tcl,
But before I prompt VMD, I source gromacs as below:
how can I solve this problem?
Best regards
Jinyoung
I tried to visualize the MARTINI force field system with VMD by using cg_bonds.tcl
When I used cg_bonds.tcl,
vmd > cg_bonds -top system.top
key "na" not known in dictionary
vmd > cg_bonds -tpr ../PROD/prod_1.tpr
couldn't execute "/usr/bin/gmxdump": no such file or directoryBut before I prompt VMD, I source gromacs as below:
source ~/apps/GROMACS/gromacs-2020.4_gcc-7.5.0_openmpi-4.0.2/bin/GMXRChow can I solve this problem?
Best regards
Jinyoung
Last edit: 2 years 7 months ago by Jinyoung.
Please Log in or Create an account to join the conversation.
- riccardo
-
- Offline
- Platinum Boarder
2 years 7 months ago #9112
by riccardo
Replied by riccardo on topic problem encounterd when I used cg_bonds.tcl
This is a problem pf cg_bonds with newer Gromacs version. cg_bonds is looking for "gmxdump" which was renamed in recent Gromacs version.
Try using the following:
*NOTE* that your path to "gmx" might be different! Look for where Gromacs is installed and where that "gmx" file is.
Try using the following:
cg_bonds [b]-gmx /usr/local/gromacs/bin/gmx[/b] -tpr ...*NOTE* that your path to "gmx" might be different! Look for where Gromacs is installed and where that "gmx" file is.
Please Log in or Create an account to join the conversation.
- Jinyoung
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 14
2 years 6 months ago #9156
by Jinyoung
Replied by Jinyoung on topic problem encounterd when I used cg_bonds.tcl
I installed gromacs-5.1 but I encounterd another problem...
The error message is below
child process exited abnormally
The error message is below
child process exited abnormally
Please Log in or Create an account to join the conversation.
- Jinyoung
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 14
2 years 6 months ago #9157
by Jinyoung
Replied by Jinyoung on topic problem encounterd when I used cg_bonds.tcl
I installed gromacs-5.1 but I encounterd another problem...
The error message is below
child process exited abnormally
The error message is below
child process exited abnormally
Please Log in or Create an account to join the conversation.
- Jinyoung
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 14
2 years 6 months ago #9158
by Jinyoung
Replied by Jinyoung on topic problem encounterd when I used cg_bonds.tcl
I installed gromacs-5.1 but I encounterd another problem...
The error message is below
child process exited abnormally
The error message is below
child process exited abnormally
Please Log in or Create an account to join the conversation.
- Jinyoung
-
Topic Author
- Offline
- Fresh Boarder
Less
More
- Posts: 14
2 years 6 months ago #9166
by Jinyoung
Replied by Jinyoung on topic problem encounterd when I used cg_bonds.tcl
I installed gromacs-5.1 but I encounterd another problem...
The error message is below
child process exited abnormally
The error message is below
child process exited abnormally
Please Log in or Create an account to join the conversation.
- riccardo
-
- Offline
- Platinum Boarder
2 years 4 months ago #9254
by riccardo
Replied by riccardo on topic problem encounterd when I used cg_bonds.tcl
It would be useful if you specified the command you used.
Please Log in or Create an account to join the conversation.
Time to create page: 0.103 seconds