Thank you justin..<br>I solve script problem..<br><br> I have another query ..<br> As mention in tutorial , In step six , we have to do brief NPT equilibration <br> npt_umbrella.mdp link is <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/Files/npt_umbrella.mdp">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/Files/npt_umbrella.mdp</a><br>
After these we have to run MD ...mdp file link is <br> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/Files/md_umbrella.mdp">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/Files/md_umbrella.mdp</a><br>
<br><br>1. In both case define is same..<br> In general When we are doing NPT we are position restrain whole protein backbone ,<br> But in these case we are only restrain chain B...Please explain in detail ...<br>
<br>2. The difference in mdp file is at gen_vel, and run time 100 ps for npt , 10 ns for md <br> If both mdp file is same Then why to do separate npt and md <br><br> ( Is the only reason is to generate velocity in npt simulation ??? Why we are not using velocity from <br>
pull <i>(step five)</i> ) <br><br>3 . If we are using the gen_vel = yes <br> continuation = yes <br> <br> If continuation is yes, then why gen_vel is yes ????<br><br>Please shade some light on meaning of continuation and gen_vel <br>
<br><br>Thank you in advance<br><br> <br>With Best Wishes,<br>Rama David <br>