[gmx-users] Timestep and force field

[varsha gautham]

Dear gmx user,


Am a beginner to gromacs,I have a few questions to be clarified before
getting started with gromacs.

1.on giving pdb2gmx gromacs offers force fields fom 0 to 6 and also i
read like opls-aa is the best forcefield for protein? why is that
so?What kind of forcefield do i have to choose for a protein? how are
various forceields differ?

2.Then regarding the water models I have read various materials ,but
still the concept is not clear to me. what are  all
these,SPC,TIP3P,TIP4P,TIP5P,?
It will be very helpful if someone explain me what are all these and
how they differ and which water model is best suited for a protein?


3. hen how to choose a timestep for a simulation like a picosecond or
a nanosecond?What is a timestep?

I have gone through many materials and stuffs related to Gromacs.But i
dint get a clear idea, addressing this 2 questions.I will be really
thankful if someone took time to read to this mail patiently and reply
me with a solution which am looking for months together.Thanks in
advance.

-varsha