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 >> [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 > _______________________________________________ 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
