Dear Sir, <br><br> Thanks for your reply. <br><br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
It means "not a number." I've never seen that before from g_energy, but based on the extremely small error estimates, especially for the temperature, I'd suspect you're using extremely tight coupling which may be causing some error.</blockquote>
<div><br>I was thinking such errors come when there are some infinite values. This same<br>mdp file parameters I have used to run 3 more simulations in different systems. <br>But that was all fine, such "nan" error was not present.<br>
</div><div> <br>
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The RMSD presented by g_energy is the standard deviation of the data analyzed. It is unrelated to the RMSD of the protein.</blockquote><div><br>Yes that is true. I just checked it to make sure that there is no horrible errors in <br>
the trajectory.<br><br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
In a periodic system, there is no such thing as "inside" and "outside" since the system is infinite.<br></blockquote><div><br>Than is true. but why mentioned is that when we are analyzing we take into <br>
account only one of the unit cell not infinite. By outside I meant out of the unit <br>cell in consideration into a periodic image.<br><br>
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trjconv -pbc mol -ur compact (and -center if you like).</blockquote><div><br>Thank you I will try it out.<br><br>
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Never used ngmx, but with the trjconv command I've stated everything should show up quite nicely in VMD :)<br></blockquote><div><br>Ok thanks. I am new to VMD need to explore it more.<br> <br>Thanking you<br>With Regards<br>
M. Kavyashree</div><br></div><br>