Ignoring the fact that one of them is commercial and one is not both Amber and Gromacs are very resourceful ( packages and tools ). I have tried tutorial of both amber and gromacs and I find gromacs more comfortable given that the documentations and tutorials are well maintained and more elaborated. However, I will like to know the ups and downs and power and limitations of both framework.
Looks like from a beginners point of view, gromacs is the goto.
From a long term perspective, which is a better choice? (AMBER or GROMACS) . Kindly share your experience.
Considering that the AmberTools include the sander simulation engine, both are free of charge actually. The major difference is that the GPU enabled amber binary PMEMD must be bought.
In regards of performance, gromacs is far in front of sander. But features and maintainance are much better on the amber site. An example is the current lack of implicit solvent in gromacs, which was broken due lots of code clean up and re-design. Currently lot's of features are dismissed out of the code beacause nobody can maintain it the way it has developed the past years.
Generally there is no reason to rely on only one tool or package since all packages have their advantages and disadvantages but usually play together nicely. E.g. you can use ambers xleap to build a system, but simulate it with gromacs at the end.
At our site btw. we use e.g. AmberTools, Parmed, Gromacs, NAMD, VMD, depending on what we want to do. .
Best wishes
I am totally agreed with Dr. Geist’s opinion.
GROMACS is attractive due to its strong user-base, scalability and parallel implementation. You may choose any one (GROMACS or AMBER) as per your research interest.
I am totally agree with Dr Geist. Amber interface and amber community are very very un-friendly. Also with ATB server you can create a new forcefield very easily just by uploading your pdb file for gromacs, in amber to do this you have to use gaussian, vffdt, paramfit, sander exc.. and you have to waste more than 1 week.
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