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
--
"Feel free" - 10 GB Mailbox, 100 FreeSMS/Monat ...
Jetzt GMX TopMail testen: http://www.gmx.net/de/go/topmail
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
"Feel free" - 10 GB Mailbox, 100 FreeSMS/Monat ...
Jetzt GMX TopMail testen: http://www.gmx.net/de/go/topmail
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before
posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
