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I need a GUI front-end simple MD software for OS X, something similar to ascalaph maybe.

What I need to do is a rigid optimization of waters around a protein. I don't have many water molecules around, so a few tips about how to not let them fly away would be nice too.

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  • $\begingroup$ Could you put your protein an waters in "box" so they're forced to stay within some distance of your protein? $\endgroup$ Oct 12, 2015 at 2:38
  • $\begingroup$ yes, I still would like to do an energy minimisation. $\endgroup$ Oct 12, 2015 at 10:37

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I'm biased, but I recommend Avogadro which can do simple force field optimization using MMFF94 or GAFF. It's not MD, but it would certainly work. It runs on Mac.

The water molecules shouldn't "fly away" during minimization, since there should be hydrogen-bond and Van der Waals terms attracting them to each other and to the protein.

I'll also point out that VMD runs on Mac and are quite easy to use. It can set up MD calculations with NAMD, GROMACS, etc.

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  • $\begingroup$ I agree with VMD. That's a great choice! $\endgroup$ Nov 2, 2015 at 18:08

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