David, > Both your gro files are wrong, the definition of gro files has never > changed. Do you mean to say this has ever worked?
Yes, it worked fine in 3.3.x. I would point out that trjconv has an -ndec option which, if used to output a gro file, will generate high-precision gro files as output. Presumably these are acceptable gro files?!? What exactly is wrong with it? Here's one that works (an output with -ndec from trjconv); I'm not clear on why this one works and the one I sent doesn't: Generated by trjconv : 9 system in water t= 0.00000 17 1ASN C4 1 20.166000366211 20.479019165039 20.427963256836 0.0000000000000 0.0000000000000 0.0000000000000 1ASN H1 2 20.146055221558 20.570739746094 20.372158050537 0.0000000000000 0.0000000000000 0.0000000000000 1ASN H2 3 20.098955154419 20.395944595337 20.404985427856 0.0000000000000 0.0000000000000 0.0000000000000 1ASN H3 4 20.166000366211 20.499057769775 20.535308837891 0.0000000000000 0.0000000000000 0.0000000000000 1ASN C7 5 20.295000076294 20.426000595093 20.385000228882 0.0000000000000 0.0000000000000 0.0000000000000 1ASN O1 6 20.315000534058 20.309999465942 20.349000930786 0.0000000000000 0.0000000000000 0.0000000000000 1ASN N2 7 20.393997192383 20.515981674194 20.393993377686 0.0000000000000 0.0000000000000 0.0000000000000 1ASN H4 8 20.489086151123 20.482969284058 20.386993408203 0.0000000000000 0.0000000000000 0.0000000000000 1ASN H5 9 20.374940872192 20.611291885376 20.421081542969 0.0000000000000 0.0000000000000 0.0000000000000 2SOL OW 10 20.548002243042 20.120998382568 20.291999816895 0.0000000000000 0.0000000000000 0.0000000000000 2SOL HW1 11 20.500000000000 20.046926498413 20.254966735840 0.0000000000000 0.0000000000000 0.0000000000000 2SOL HW2 12 20.479961395264 20.183086395264 20.318038940430 0.0000000000000 0.0000000000000 0.0000000000000 2SOL MW 13 20.535623550415 20.119720458984 20.290826797485 -0.0009536742582 0.0000000000000 0.0000000000000 3SOL OW 14 20.242019653320 20.178009033203 20.123998641968 0.0000000000000 0.0000000000000 0.0000000000000 3SOL HW1 15 20.164087295532 20.143032073975 20.167186737061 0.0000000000000 0.0000000000000 0.0000000000000 3SOL HW2 16 20.300615310669 20.201835632324 20.195838928223 0.0000000000000 0.0000000000000 0.0000000000000 3SOL MW 17 20.239955902100 20.176818847656 20.136268615723 -0.0085830679163 -0.0038146970328 0.0000000000000 40.642551422119 40.642551422119 40.642551422119 Maybe this is just wishful thinking, but it would be nice if the manual actually explained the specifications of the gro file format. For example, it is clearly not fixed-width, as the number of digits in the columns can vary, but at the same time it doesn't appear to be tab/space delimited, as the columns of velocities can occasionally run together (if I'm using the -ndec option, especially). Obviously one can look at the code (perhaps I should do this) but it seems it should be documented. Thanks, David > If you want high precision use g96. > >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > David van der Spoel, Ph.D., Professor of Biology > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755. > sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se > _______________________________________________ > 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 gmx-users-requ...@gromacs.org. > 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php