<span dir="ltr"></span><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Ragnarok sdf wrote:<br>
> Is the RMSD given by g_energy -f -f2 in Joule or KJoule?<br>
<br>
Units are described in section 2.2 of the manual. For g_energy, the<br>
units will obviously depend on the quantity involved.<br>
<br>
Mark<br>
<br>
</blockquote></div>Well, that is the reason of my question. My FEP step when analysed with "echo 10 0 | g_energy -f input1.edr -f2 input1-2.edr" gives out.<br><br>Statistics over 99901 steps [ 50.0000 thru 249.8000 ps ], 1 data sets<br>
All averages are exact over 99901 steps<br><br>Energy Average RMSD Fluct. Drift Tot-Drift<br>-------------------------------------------------------------------------------<br>Potential -283288 482.39 477.927 1.13508 226.792<br>
Opened r1_fep015-020.edr as single precision energy file<br>Reading energy frame 1200 time 240.000 <br>Back Off! I just backed up runavgdf.xvg to ./#runavgdf.xvg.1#<br><br>Energy dF = -kT ln < exp(-(EB-EA)/kT) >A<br>
Potential 5.12819<br><br>I know the potential of 5.12819 given for this specific step is in kJ, and that this is the actual resul of my deltaG for this step. But is the RMSD value given also for this difference, or it has nothing to do with it? If so, g_analyse could analyse my "runavgdf.xvg" resultant from this run, but obviously it would give a slightly different result because g_energy uses the full precision trajectorie energy file. So, in this case, how would I obtain the RMSD of my result?<br>
<br>Fabrício Bracht<br>