> [EMAIL PROTECTED] 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 >> _______________________________________________ >> gmx-users mailing list [email protected] >> http://www.gromacs.org/mailman/listinfo/gmx-users >> 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 > 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 > [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
