[gmx-users] kind of contacts in protein-dna interaction during simulation

Mark Abraham 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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