hi, I prefer AMBER because you can obtained different out put and fixing errors in AMBER is easier than other software.

Both GROMACS and AMBER has its uniqueness. You can use GROMACS because very simple command line and most of the analysis codes are inbuilt, and need not put much efforts. In case of AMBER, many kinds of tutorials and inbuilt options are available such as steered MD, QM/MM simulation, DFT simulations etc. available. But, in GROMACS you need to patch the external codes with GROMACS. So, depend on your need you can choose.

Thank you so much! your reasons are very good for me.

Take into account that AMBER refers both to the software and the force field family that is mostly associated with the code.

Personally, if I were to use the AMBER family of force fields I would probably use the AMBER code, as it is probably built to run that force field family in a privileged way. Additionally, most of the available resources for the code will address specifically this force field family and its problems.

On the other hand, if I were to use a different force field, such as the OPLS family, I would probably use GROMACS over other alternatives. I think it is a generally well built suite.

See there is nothing as such to be quoted as a good or a bad force field, be it AMBER, be it CHARMM. I have worked on both, and all i can say is one could find either of the methods convinient as per the lab history or the materials/tutorials being followed. All one would get is different schemes of working and hence different energy values. But that cant be the a scaling factor for the differentiation.

Also by following the specific literature regarding your research work, you could see what people have preffered and accordingly you may also decide.

You may also visit the following link:

http://www.gromacs.org/About_Gromacs

All the best.

Thank you very much.

I would be glad if others have comments on this case.

Best regards.

Dear,

Both are very good for the Molecular Dynamics (MD). However, AMBER is more intuitive when you have to deal with inorganic compounds. So, it depends on your own system.

Cheers,

Emanuele