[gmx-users] warning message while using eneconv

[sunita at chem.iitb.ac.in]

> sunita at chem.iitb.ac.in wrote:
>> Dear users,
>> I am using gromacs version 3.2.1. While concatinating .edr files using
eneconv, I am getting warning messages. The concatinated file when used
for     analysis, it continues to give the same warning messages. The
final .xvg output seems to be correct.
>> I never had this kind of problem with gromacs version 3.1.4.
>> Is there any problem with the concatinated .edr file?
>> How to fix this problem?
>> The waring messages are
>> ===========================================
>> WARNING: there may be something wrong with energy file ../200ns.edr
Found: step=-2124237637, nre=71, ndisre=0, nblock=0, time=124900.
Trying to skip frame expect a crash though
>> WARNING: there may be something wrong with energy file ../200ns.edr
Found: step=-2124237387, nre=71, ndisre=0, nblock=0, time=124900.
Trying to skip frame expect a crash though
>> WARNING: there may be something wrong with energy file ../200ns.edr
Found: step=-2124237137, nre=71, ndisre=0, nblock=0, time=124901.
Trying to skip frame expect a crash though
>> WARNING: there may be something wrong with energy file ../200ns.edr
Found: step=-2124236887, nre=71, ndisre=0, nblock=0, time=124901.
Trying to skip frame expect a crash though
>> ===========================================
>> With regards,
>> sunita
>> _______________________________________________
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> have you run gmxcheck?

gmxcheck does not show any error except at times it shows warning message
because of the extension of the crashed run after that point.


>
> maybe you can enevonc the whole file once more, possibly with the
-settime flag.

I checked with the -settime flag still getting the same warning message.
>
I am writing you in detail so that it will be easier for you to find the
exact problem.

I have sub fragments of 2ns edr files which are generated by MD run. I
tried concatinating the 2ns .edr files. It was doing fine but after 160ns
I got the message that something wrong with the .edr files.
Then I thought there may be some problem and then just concatinated and
made 10ns edr files such as 150-160ns.edr and 160-170ns.edr. By doing this
I didn't have any problem. Finally I generated all 10ns edr files for a
total of 600ns.

To get final concatinated 600ns.edr, when I concatinated all the 10ns edr
files (0-10ns.edr, 10-20ns.edr 20-30ns.edr ... and  so on) again I got the
same warning messages.

For generating same shorter .edr fragments (such as 0-10ns, 10-20ns...etc)
eneconv doesn't give any warning message but for longer fragment (600ns)
why it gives such messages.

With regards,
Sunita



>
> --
> David.
> ________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept.
of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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