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normal Should I fill in the Backbone and SideChain groups in an index file for MD?

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2 years 11 months ago #8943 by hawo
Should I fill in the Backbone and SideChain groups in an index file for MD? was created by hawo
Hello everyone. I'm simulating a system that consists of a protein and a number of small molecules in a water box. During equilibration and production runs, I supply an index file made with make_ndx, but by default it treats all protein beads as side-chain. Does it matter? Should I edit the index file to explicitly define BB beads as backbone and SCi beads as side-chain?

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2 years 11 months ago #8944 by riccardo
Replied by riccardo on topic Should I fill in the Backbone and SideChain groups in an index file for MD?
Hi. This really depends on: what you are using the index file for?

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2 years 11 months ago #8947 by hawo
Replied by hawo on topic Should I fill in the Backbone and SideChain groups in an index file for MD?
Frankly, I'm just using index files because the tutorial for small molecule binding suggests that I should.

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2 years 11 months ago #8948 by hawo
Replied by hawo on topic Should I fill in the Backbone and SideChain groups in an index file for MD?
Oh, I remembered: I'm actually using it for temperature coupling.

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2 years 11 months ago #8964 by riccardo
Replied by riccardo on topic Should I fill in the Backbone and SideChain groups in an index file for MD?
I'd say if it's for temperature coupling you want all the protein beads to be coupled together in the same group.

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