normal DNA with polarized water

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2 years 10 months ago #5727 by shibalagu
DNA with polarized water was created by shibalagu
Dear all,

I am trying to simulate DNA in polarized water. Therefore I assume I should use the polarized force field for DNA, martini_V2.1P-dna.itp, am I right?

And if I want to use this force field, when I generate the coarse-grained model with this command:

python martinize-dna.py -f dna.gro -x dna.cg.pdb -o dna.cg.top -dnatype ds-stiff

Should I add another flag: -ff martini21p? Or I just need to edit "dna.cg.top", and include "martini_V2.1P-dna.itp"

Thank you very much.

Zhenhai

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2 years 10 months ago #5746 by jaakko
Replied by jaakko on topic DNA with polarized water
Hi Zhenhai,

Nothing changes in the DNA itp file depending on the water model used and thus you don't need any extra flags. Just change the martini itp file to the one you mentioned by adjusting the top.

- Jaakko

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2 years 9 months ago #5770 by shibalagu
Replied by shibalagu on topic DNA with polarized water
Hi Jaakko, Thank you very much!

Zhenhai

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