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Stiff RNA + ElneDyn for large RNA
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2 years 5 months ago #9233
by mandar
Stiff RNA + ElneDyn for large RNA was created by mandar
Hello Everyone,
I am building CG model of large ribosomal RNA with martinize-nucleotide.py script provided in tutorial folder. I wish to use Stiff elastic network as performed in the MARTINI RNA paper.
I could not find the extra parameters added to topology or itp file after providing -elastic and -ef 1000 option. So, I do not understand how elastic network is handled in MARTINI simulation.
It will be great if I can get some pointers about building stiff elastic network topology with martinize-nucleotide.py script?
Thanks and Regards,
Mandar Kulkarni
I am building CG model of large ribosomal RNA with martinize-nucleotide.py script provided in tutorial folder. I wish to use Stiff elastic network as performed in the MARTINI RNA paper.
I could not find the extra parameters added to topology or itp file after providing -elastic and -ef 1000 option. So, I do not understand how elastic network is handled in MARTINI simulation.
It will be great if I can get some pointers about building stiff elastic network topology with martinize-nucleotide.py script?
Thanks and Regards,
Mandar Kulkarni
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2 years 5 months ago #9234
by mandar
Replied by mandar on topic Stiff RNA + ElneDyn for large RNA
Hi,
I found the options for stiff elastic network as -type ss-stiff -ff elnedyn22nucleic -elastic.
Regards,
Mandar Kulkarni
I found the options for stiff elastic network as -type ss-stiff -ff elnedyn22nucleic -elastic.
Regards,
Mandar Kulkarni
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