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DNA with polarized water
- shibalagu
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7 years 9 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
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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- jaakko
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7 years 9 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
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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- shibalagu
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7 years 8 months ago #5770
by shibalagu
Replied by shibalagu on topic DNA with polarized water
Hi Jaakko, Thank you very much!
Zhenhai
Zhenhai
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