Hello MPID (?),<div><br></div><div>Sorry, I did not see your first message.</div><div><br></div><div>For the tpic algorithm, the coordinate of insertion is the last coordinate (after the particle to be inserted) in the .tpr you give for the mdrun -rerun. Hence, you should create a structure file (.gro) with the original system, followed by the particle to be inserted, and lastly, the coordinate of insertion. Run this structure file through grompp to generate a .tpr file, which you shall give to mdrun.</div>
<div><br></div><div>I hope this has helped.</div><div><br></div><div>Best,</div><div>Joćo<br><br><div class="gmail_quote">On Sun, Mar 4, 2012 at 10:43 PM, MPID <span dir="ltr"><<a href="mailto:mpmcgovern@wisc.edu" target="_blank">mpmcgovern@wisc.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
If no one knows this, does anyone know the best way to add a coordinate to a<br>
trajectory in general?<br>
<br>
--<br>
View this message in context: <a href="http://gromacs.5086.n6.nabble.com/Test-particle-insertion-extra-coordinate-tp4536816p4546083.html" target="_blank">http://gromacs.5086.n6.nabble.com/Test-particle-insertion-extra-coordinate-tp4536816p4546083.html</a><br>
<div><div>Sent from the GROMACS Users Forum mailing list archive at Nabble.com.<br>
--<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>Joćo M. Damas<br>PhD Student<br>Protein Modelling Group<br>ITQB-UNL, Oeiras, Portugal<br>Tel:<a href="tel:%2B351-214469613" value="+351214469613" target="_blank">+351-214469613</a><br>
</div>