<div> </div>
<div class="gmail_quote">On Wed, Feb 2, 2011 at 3:15 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="im">On 3/02/2011 6:15 AM, Sai Pooja wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">The problem is solved with grompp i.e. I use the -t .cpt option. However, now appending does not work. I remember Mark said in a previous mail that a certain environment variable can allow appending to happen even in such cases. I would liek to try that out.<br>
<br></blockquote></div>No, I said that an environment variable can override the mechanism that blocks ensemble changes in mdrun.
<div class="im">
<div></div></div></blockquote>
<div> </div>
<div>So how can I use this environment variable.. I might be asking an absurd question since I don't really understand what an environment variable is. But I would definitely liek to experiment with it, since I am in the process of trying out these different options and figuring out which would be the best.</div>
<div> </div>
<div>I also need to understand something. What exactly does the tpbconv do when only -s and -nsteps or -extend options are supplied - it seems that it takes all the information(mass, topology, restraints) from the previous tpr file and just changes the init_step parameter and the number of steps till which the simulation should run.</div>
<div> </div>
<div>Now if that is the case, I am still unable to understand that if the cpt file is NOT provided to mdrun (or a mismatched one is provided), how does mdrun obtain the coordinates, velocities, box-dimensions of the last frame. If it doesn't use the ones of the last frame, what does it really use?</div>
<div> </div>
<div>If it gets them from the new_tpr file, and the new_tpr file gets it from previous_tpr file via tpbconv, then how does that ensure continuation from the last frame, because the previous_tpr file might have been compiled even before the simulation started. And as far as I know, it is purely an input file to mdrun and has no information on the last coordinates/velocities of the mdrun.</div>
<div> </div>
<div>You may have answered this before but I have tried and failed in understanding. I would request you to help me in understanding the above. I would really appreciate it.</div>
<div> </div>
<div>Regards</div>
<div>Pooja</div></div>