Dear users, I would like to carry out steered molecular dyanmics simulations on one of my protein dimer. I have a few questions to learn regarding this.
1. The mdrun program needs -pn index.ndx file The way I understand is, we need to create the index file with groups (say atom1 to which the spring has to be attached and the atom 2 which I would like to fix). These are the names (I mean what ever the names I give for the groups in the index file) do I need to mention at group_1 and group_2 in pull.ppa ?? I believe the index file can be prepared in the same way as we do in conventional MD simulations. 2. Its a general question. What usually the rates people does use for spring motions ? 3. I donot have experimental AFM studies on my system so how can I choose the optimum force ? 4. I want to pull the atom along the "Z" direction. I belive afm_dir1 = 0 0 1 5. How can I mention the initial spring positoins ?? i.e., afm_init1 ?? I looked for a few tutorials on this but i do not have any luck. If somebody finds some stuff regarding this could you please share the links with me ?? Thanks. Ram.
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