[gmx-users] Re: gmx-users Digest, Vol 65, Issue 104

Ragnarok sdf fabracht1 at gmail.com
Thu Sep 17 21:49:03 CEST 2009

> Ragnarok sdf wrote:
> > Is the RMSD given by g_energy -f -f2 in Joule or KJoule?
> Units are described in section 2.2 of the manual. For g_energy, the
> units will obviously depend on the quantity involved.
> Mark
> 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.

Statistics over 99901 steps [ 50.0000 thru 249.8000 ps ], 1 data sets
All averages are exact over 99901 steps

Energy                      Average       RMSD     Fluct.      Drift
Potential                   -283288     482.39    477.927    1.13508
Opened r1_fep015-020.edr as single precision energy file
Reading energy frame   1200 time  240.000
Back Off! I just backed up runavgdf.xvg to ./#runavgdf.xvg.1#

Energy                   dF = -kT ln < exp(-(EB-EA)/kT) >A
Potential                   5.12819

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?

Fabrício Bracht
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