Berk, > I checked the gro manual page: > http://www.gromacs.org/documentation/reference_4.0/online/gro.html > and found out that it is actually pretty clear. > Note that it is fixed format, but with flexible precision which is derived > from the space between the decimal points.
Thanks. I was looking at the 3.3 paper manual. > I found out a while ago that in 3.3 gro was not read fixed format, > but in some messy way which was close to free format for the coordinates. > For 4.0 I changed the reading so it is really fixed format and one > can store coordinates of 1000 nm or larger and -100 nm and smaller. OK, that's good to know. > Note that the different precision gro files do not adhere to the original > GROMOS format and might not be read correctly by some software. Thanks, David > Berk > >> Date: Wed, 11 Feb 2009 10:46:26 -0600 >> Subject: Re: [gmx-users] funny zero-step mdrun results in 4.0.3 >> From: dmob...@gmail.com >> To: gmx-users@gromacs.org >> >> 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 > > ________________________________ > Express yourself instantly with MSN Messenger! MSN Messenger > _______________________________________________ > 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