Hi Gromacs Friends,<br> <br> I am doing Justin-Umbrella sampling tutorial...<br><a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/06_umbrella.html</a><br>
<br>After pulling I found the Chain A is moving away from protofibril but reaches up to the other end of the cell..<br>So Is these situation Satisfy the Minimum image condition??? or Am I doing some wrong ..???<br><br>as tutorial Says..<br>
<font face="Arial"><font size="3">GROMACS calculates distances while
simultaneously taking periodicity into account. This, if you have a
10-nm box, and you pull over a distance greater than 5.0 nm, the
periodic distance becomes the reference distance for the pulling, and
this distance is actually less than 5.0 nm! This fact will
significantly affect results, since the distance you <b>think</b> you are pulling is not what is <b>actually</b> calculated.</font></font> <br><br>My Query is on very basic concept...<br> tutorial says....<br><font face="Arial"><font size="3"><br>
In this example, we will be sampling
COM distances from 0.5 - 5.0 nm along the z-axis using roughly 0.2-nm
spacing. The following example commands may or may not be literally
correct (the frame numbers may differ), but will serve as an example as
to how to run grompp on separate coordinate files to generate all 23
inputs (note as well that 23 is the amount of windows required to obtain
0.2-nm spacing over roughly 4.5 nm;</font></font><br>my summary_distances.dat has following lines..<br><br>0 0.5011713<br>1 0.5068762<br>2 0.4948514<br>..<br>.<br>.<br>160 0.6993698<br>so my 1st configuration will be at 0 (0.5011713) and 160 (0.69936) .Is it right???<br>
<br>I choose total 28 windows instead of 23 ...So is it good or bad ???<br><br>Thank you in Advance...<br>With Best Wishes,<br>Rama David<br>