Dear Friends,
I badly want to learn nucleic acid simulation could anyone please guide me how to begin the learning with? I have installed NAMD and went through the ubq tutorial given in net. However i couldn't understand the basics behind editing the configuration file. How should i start nucleic acid simulation. . Please help! And how to know the difference in simulation parameter of nucleic acid and a protein?
Thanks in advance
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written
by
grosy •
1 answer
I would pick up a recent paper that reviews MD simulations for NA molecules, like this one, and get from there a few hints on where to start looking. Then, I would pick a paper that describes MD simulations of a system similar to yours (do you have double strands? single strands? RNA? DNA?) and essentially try their parameters (adjusting where and if necessary).
I don't know :) I meant 'check what you have and look for papers that kind of do the same'.
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