gromacs 5 support problem for Martini tutorials: polymers
- duyu
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7 years 1 day ago #7204
by duyu
gromacs 5 support problem for Martini tutorials: polymers was created by duyu
Dear Martini Users,
I'm following the Martini tutorials: polymers . I used the command
`echo "bonds_core" | gmx_mpi distance -f traj_cg.xtc -len 0.35 -tol 0.8 -n bonds.ndx -oh bonds.xvg`
to replace the original
`g_bond -f traj_cg.xtc -blen 0.35 -tol 0.8 -n bonds.ndx -o bonds.xvg`.
But Abort (core dumped) occured.
Would you please give some advice to use gromacs 5 to study the tutorial?
Thanks for your reply.
I'm following the Martini tutorials: polymers . I used the command
`echo "bonds_core" | gmx_mpi distance -f traj_cg.xtc -len 0.35 -tol 0.8 -n bonds.ndx -oh bonds.xvg`
to replace the original
`g_bond -f traj_cg.xtc -blen 0.35 -tol 0.8 -n bonds.ndx -o bonds.xvg`.
But Abort (core dumped) occured.
Would you please give some advice to use gromacs 5 to study the tutorial?
Thanks for your reply.
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- riccardo
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6 years 11 months ago #7209
by riccardo
Replied by riccardo on topic gromacs 5 support problem for Martini tutorials: polymers
The 'translation' of the command to GMX 5 looks correct. Perhaps something else is going wrong?
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- dengjinxia
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6 years 11 months ago #7210
by dengjinxia
Replied by dengjinxia on topic gromacs 5 support problem for Martini tutorials: polymers
I am playing wtih tutorial as well, but can not find the mapping.ndx, wonder where it is provided and how to get it.
Thanks,
Nancy
Thanks,
Nancy
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- riccardo
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6 years 11 months ago #7216
by riccardo
Replied by riccardo on topic gromacs 5 support problem for Martini tutorials: polymers
From the tutorial:
"[...]. As you can imagine for a system such as ours this index file requires a bit of scripting to prepare as there'll be 2000 groups (or as many CG beads as your mapping yields). The script indexer.py will do this for you, but edit it to understand its workings and to ensure its parameters are correct for the mapping you chose. [...]"
In the archive "PEG_parametrization.tgz", which you can download from the tutorial page, there's a python scripty "indexer.py" which you can run as:
python indexer.py
This will generate the index "mapping.ndx". As recommended in the tutorial, please study the script and potentially edit it to get different mappings.
"[...]. As you can imagine for a system such as ours this index file requires a bit of scripting to prepare as there'll be 2000 groups (or as many CG beads as your mapping yields). The script indexer.py will do this for you, but edit it to understand its workings and to ensure its parameters are correct for the mapping you chose. [...]"
In the archive "PEG_parametrization.tgz", which you can download from the tutorial page, there's a python scripty "indexer.py" which you can run as:
python indexer.py
This will generate the index "mapping.ndx". As recommended in the tutorial, please study the script and potentially edit it to get different mappings.
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- dengjinxia
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6 years 11 months ago #7217
by dengjinxia
Replied by dengjinxia on topic gromacs 5 support problem for Martini tutorials: polymers
thanks, works well :-)
Nancy
Nancy
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- dengjinxia
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6 years 11 months ago #7218
by dengjinxia
Replied by dengjinxia on topic gromacs 5 support problem for Martini tutorials: polymers
Hi All,
I am playing with the martini bilayer tutorial. It has two erros at the step of minimization, as well as production phase:
ERROR 1 : With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported ERROR 1 [file martini_md.mdp]: With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported I used the .mdp files provided in the .zip. So wonder whether someone can share a valid version for me to progress the tutorials :-) thanks a lot. nancy[file martini_md.mdp]:
With Verlet lists only cut-off, reaction-field, PME and Ewald
electrostatics are supported
ERROR 1 : With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported I used the .mdp files provided in the .zip. So wonder whether someone can share a valid version for me to progress the tutorials :-) thanks a lot. nancy[file martini_md.mdp]:
With Verlet lists only cut-off, reaction-field, PME and Ewald
electrostatics are supported
I used the .mdp files provided in the .zip. So wonder whether someone can share a valid version for me to progress the tutorials :-)
thanks a lot.
nancy
I am playing with the martini bilayer tutorial. It has two erros at the step of minimization, as well as production phase:
ERROR 1 : With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported ERROR 1 [file martini_md.mdp]: With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported I used the .mdp files provided in the .zip. So wonder whether someone can share a valid version for me to progress the tutorials :-) thanks a lot. nancy[file martini_md.mdp]:
With Verlet lists only cut-off, reaction-field, PME and Ewald
electrostatics are supported
ERROR 1 : With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported I used the .mdp files provided in the .zip. So wonder whether someone can share a valid version for me to progress the tutorials :-) thanks a lot. nancy[file martini_md.mdp]:
With Verlet lists only cut-off, reaction-field, PME and Ewald
electrostatics are supported
I used the .mdp files provided in the .zip. So wonder whether someone can share a valid version for me to progress the tutorials :-)
thanks a lot.
nancy
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- peterkroon
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6 years 11 months ago #7219
by peterkroon
Replied by peterkroon on topic gromacs 5 support problem for Martini tutorials: polymers
You can use the one you find here:
cgmartini.nl/images/parameters/exampleMDP/martini_v2.x_new.mdp
Adapt where necessary!
Adapt where necessary!
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