[gmx-users] warning message while using eneconv

[sunita at chem.iitb.ac.in]

Dear David,

Thanks for your reply.
pls suggest how to get rid of these warning messages.
I do not find where is the mistake.

Thank you very much.
sunita



>> 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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