Dear users,<br><br>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.<br><br>1. The mdrun program needs -pn index.ndx file<br><br>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.<br>
<br>2. Its a general question. What usually the rates people does use for spring motions ?<br><br>3. I donot have experimental AFM studies on my system so how can I choose the optimum force ?<br><br>4. I want to pull the atom along the "Z" direction. I belive afm_dir1 = 0 0 1<br>
<br>5. How can I mention the initial spring positoins ?? i.e., afm_init1 ??<br><br>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 ??<br>
<br>Thanks.<br>Ram.<br>