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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php