[gmx-users] kind of contacts in protein-dna interaction during simulation
Mark.Abraham at anu.edu.au
Sun Nov 7 15:10:30 CET 2010
On 7/11/2010 9:36 PM, leila karami wrote:
> Dear Mark
> thanks for your attention.
> I read manual before. I know that g_hbond is for hydrogen bond analysis. But I don’t know about Van der Waals interactions analysis and how to obtain percentage of them.
If you're planning to copy someone else's analysis, then you should be
able to do so from their description. That's why they wrote the paper...
If they don't make a description, either email them to ask, or choose
someone else to copy :-). Unfortunately, "van der Waals interactions
analysis" is far too vague to be a useful target question. As your email
pointed out, there's a bunch of mathematical parameters that go into
assigning hydrogen bonds for any analysis there... Something similar
would have to apply to vdW, and the procedure for finding that out will
often lead you towards a good method for implementing it.
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