<div>Dear Gmx Users, Dear Justin</div>
<div> </div>
<div>I am wondering which approach for generating velocities in protein or protein-ligand system is a proper one:</div>
<div> </div>
<div>a) </div>
<div>NVT gen_vel = yes</div>
<div> gen_temp=298</div>
<div> gen_seed=-1</div>
<div>NPT gen_vel=no</div>
<div>MD gen_vel=no</div>
<div> </div>
<div>b) </div>
<div>
<div>NVT gen_vel = yes</div>
<div> gen_temp=298</div>
<div> gen_seed=-1</div>
<div>NPT gen_vel=no</div>
<div>MD gen_vel = yes
<div> gen_temp=298</div>
<div> gen_seed=-1</div>
<div> </div>
<div>As I always used the approach a) I saw in Justin's tutorial (Protein and ligand) b). However, in protein in water tutorial he used the approach a). I am confused, can you please help?</div>
<div> </div>
<div>Thank you.</div>
<div> </div>
<div>Steven</div></div></div>