normal gromacs 5 support problem for Martini tutorials: polymers

  • duyu
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1 year 11 months ago #7204 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.

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1 year 11 months ago #7209 by riccardo
The 'translation' of the command to GMX 5 looks correct. Perhaps something else is going wrong?

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1 year 11 months ago #7210 by dengjinxia
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

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1 year 11 months ago #7216 by riccardo
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.

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1 year 11 months ago #7217 by dengjinxia
thanks, works well :-)

Nancy

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1 year 11 months ago #7218 by dengjinxia
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

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1 year 11 months ago #7219 by peterkroon
You can use the one you find here: cgmartini.nl/images/parameters/exampleMDP/martini_v2.x_new.mdp
Adapt where necessary!

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