<br><div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Check out <a href="http://wiki.gromacs.org/index.php/Doing_Restarts">http://wiki.gromacs.org/index.php/Doing_Restarts
</a></blockquote><div><br>Thanks very much. I do understand the general restarting mechanism. It is only the first restart that was a little bit confusing<br></div><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
><br>> I just wanted to confirm if what I am doing makes sense ? Thanks very<br>> much for the help !<br><br>These two output .tpr files should be the same except for the initial<br>steps and times, unless your mol-2.mdp
file took care of that. You can<br>use gmxcheck to test for the differences.</blockquote><div><br>Sorry I did not understand ? There is no mol-2.mdp file. So, in effect the first tpbconf command should work. The velocities will be obtained from the .trr file and not the .tpr file, correct ? That is the main issue bothering me, because the .tpr file contains the initial velocities generated during the first run.
<br><br><span class="q">tpbconv -f mol-1.trr -s mol-1.tpr -e mol-1.edr -extend 200 -o mol-2.tpr<br><br></span>Thanks again,<br><br>-himanshu<br><br></div></div>