Hi,
Well there is something special, in the sense that the sum is over
just one term, so summing does not make much sense.
But also in that case it should work.
Berk.
From: Erik Lindahl <[EMAIL PROTECTED]>
Reply-To: Discussion list for GROMACS users <gmx-users@gromacs.org>
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Subject: Re: [gmx-users] g_energy sum
Date: Fri, 27 Apr 2007 13:41:11 +0200
Hi,
If you haven't done anything special such as concatenating or cutting the
energy file in parts after the simulation, I'd say it looks like a bug.
Please create an entry at bugzilla.gromacs.org , upload the tpr, and we'll
have a look at it.
Cheers,
Erik
On Apr 27, 2007, at 1:36 PM, merc mertens wrote:
hello,
i use VERSION 3.3.1. output from
g_energy -f (ener.edr) -sum -o (energy.xvg)
is similar as with the "-b 2000" flag:
Statistics over 2000001 steps [ 0.0000 thru 4000.0000 ps ], 1 data sets
Energy Average RMSD Fluct. Drift
Tot-Drift
----------------------------------------------------------------------
---------
Coul-SR:Protein-trna -0.0237376 5.19622 0 0.0118159
47.2635
Total -0.0237376 -- -- --
--
in comparison from the xvg:
@ s0 legend "Coul-SR:Protein-trna"
@ s1 legend "Sum"
0.000000 -1107.173950
100.000000 -1201.496948
200.000000 -1142.097778
300.000000 -1082.942383
400.000000 -1063.810547
500.000000 -1058.372314
600.000000 -1061.625488
700.000000 -1326.301270
800.000000 -1233.008667
900.000000 -1169.119751
1000.000000 -1082.796021
1100.000000 -1261.529175
1200.000000 -1257.951904
1300.000000 -1310.429565
1400.000000 -1251.131592
1500.000000 -1235.889893
1600.000000 -1233.731201
1700.000000 -1077.790649
1800.000000 -1134.157471
1900.000000 -1231.017334
2000.000000 -1171.813721
2100.000000 -1311.884399
2200.000000 -1142.125366
2300.000000 -1169.552979
2400.000000 -1205.442383
2500.000000 -1189.931519
2600.000000 -1148.712402
2700.000000 -1003.882751
2800.000000 -1104.013794
2900.000000 -1076.985474
3000.000000 -1131.902832
3100.000000 -1135.494995
3200.000000 -1080.656250
3300.000000 -1257.183594
3400.000000 -1138.595215
3500.000000 -1107.039062
3600.000000 -1051.498657
3700.000000 -1139.150391
3800.000000 -1070.984741
3900.000000 -1186.214600
4000.000000 -1129.730713
i think that the ener.edr only should contain only those steps listed in
the xvg.
cheers,
merc
-------- Original-Nachricht --------
Datum: Fri, 27 Apr 2007 13:04:04 +0200
Von: Erik Lindahl <[EMAIL PROTECTED]>
An: Discussion list for GROMACS users <gmx-users@gromacs.org>
Betreff: Re: [gmx-users] g_energy sum
Oops,
Sometimes it helps to read the mail. Mea culpa - forget my previous
answer, this is something else.
It could simply be a bug in g_energy; which version are you using,
and what do you get if you remove "-b 2000" (i.e. include all steps)?
Cheers,
Erik
On Apr 27, 2007, at 12:24 PM, merc mertens wrote:
hello,
when i calculate energies with
g_energy -f (ener.edr) -b 2000 -sum -o (energy.xvg)
e.g. i get this average in the log:
Statistics over 1000001 steps [ 2000.0000 thru 4000.0000 ps ], 1
data sets
Energy Average RMSD Fluct.
Drift Tot-Drift
-------------------------------------------------------------------- --
---------
Coul-SR:Protein-trna -0.0239528 0 0
0.0381909 76.3818
Total -0.0239528 -- --
-- --
but i get this in the output energy.xvg:
@ s0 legend "Coul-SR:Protein-trna"
@ s1 legend "Sum"
2000.000000 -1171.813721
2100.000000 -1311.884399
2200.000000 -1142.125366
2300.000000 -1169.552979
2400.000000 -1205.442383
2500.000000 -1189.931519
2600.000000 -1148.712402
2700.000000 -1003.882751
2800.000000 -1104.013794
2900.000000 -1076.985474
3000.000000 -1131.902832
3100.000000 -1135.494995
3200.000000 -1080.656250
3300.000000 -1257.183594
3400.000000 -1138.595215
3500.000000 -1107.039062
3600.000000 -1051.498657
3700.000000 -1139.150391
3800.000000 -1070.984741
3900.000000 -1186.214600
4000.000000 -1129.730713
the average energies from the log and the xvg do not match. does
anybody know what is wrong here?
thank you in advance,
merc
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