Hi GROMACS users,<br> I am a very novice to GROMACS.. ..<br>My question may be very simple but very important to me..!!!<br>These may be very basics...<br><br>1. What is the meaning of comm_mode and nstcomm..<br>
I read the manual but unable to digest it..so please<br> explain in more detail along with its effect on system..<br> <br>2. When I am want to study self assembly of protein what<br> should my comm_mode -linear or angular or none ??<br>
<br>3. what is the meaning of emtol in minimisation proces??<br> Should I take emtol value more or less to come to minimum energy <br> state ??? the structure on which I am working is not having any <br> crystal or NMR structure , so I need the maximum energy<br>
minimised structure<br> <br>4. When I am doing energy minimisation the gromacs shows<br> (potential energy= -2.07)<br> conjugate gradient step wise to small or no change in energy .<br> converged to machine precision in 15881 step <br>
but dindnĀ“t reach to the requested Fmax<10<br> What should to do??<br> or the structure I get is energy minimised or not..???<br> <br> please give me your valuable advice..These help me a lot <br> <br> Thank you in advace !!!<br>