Hey Justin,<br><br>thanks for your reply.<br>For gen_vel, the manual says "Generate velocities in grompp according to a Maxwell distribution at temperature gen_temp [K], with random seed gen_seed. This is only meaningful with integrator<br>
md"<br>Since the integrator I am using is sd, I put 'gen_vel no'<br>Yes you are correct, this is equilibration.<br>From what you are saying, even with sd as the integrator, I guess, I should put <br>gen_vel yes<br>
gen_temp 310 ; i want to do the simulation at 310K<br clear="all"><br>thanks<br><br>-- <br>Shyno Mathew<br>PhD student<br>Department of Chemical Engineering<br>
Columbia University<br><br>