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Hi,<br><br>It is slightly more subtle.<br>The spacing of the decimals points is correct,<br>but the last digit of x and y ends up in y and z.<br><br>Berk<br><br><hr id="stopSpelling">From: gmx3@hotmail.com<br>To: gmx-users@gromacs.org<br>Subject: RE: [gmx-users] funny zero-step mdrun results in 4.0.3<br>Date: Wed, 11 Feb 2009 18:01:31 +0100<br><br>
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Hi,<br><br>I just had a look at the gro files you mailed.<br>They have one space too little between the x and y columns and<br>the y and z columns. Or stricktly speaking according to the format,<br>the space between the x and y decimal point does not match the<br>space between the y and z decimal point.<br><br>I will add a check for this.<br><br>Berk<br><br>> Date: Wed, 11 Feb 2009 10:46:26 -0600<br>> Subject: Re: [gmx-users] funny zero-step mdrun results in 4.0.3<br>> From: dmobley@gmail.com<br>> To: gmx-users@gromacs.org<br>> <br>> David,<br>> > Both your gro files are wrong, the definition of gro files has never<br>> > changed. Do you mean to say this has ever worked?<br>> <br>> Yes, it worked fine in 3.3.x. I would point out that trjconv has an<br>> -ndec option which, if used to output a gro file, will generate<br>> high-precision gro files as output. Presumably these are acceptable<br>> gro files?!?<br>> <br>> What exactly is wrong with it?<br>> <br>> Here's one that works (an output with -ndec from trjconv); I'm not<br>> clear on why this one works and the one I sent doesn't:<br>> <br>> Generated by trjconv : 9 system in water t= 0.00000<br>> 17<br>> 1ASN C4 1 20.166000366211 20.479019165039<br>> 20.427963256836 0.0000000000000 0.0000000000000 0.0000000000000<br>> 1ASN H1 2 20.146055221558 20.570739746094<br>> 20.372158050537 0.0000000000000 0.0000000000000 0.0000000000000<br>> 1ASN H2 3 20.098955154419 20.395944595337<br>> 20.404985427856 0.0000000000000 0.0000000000000 0.0000000000000<br>> 1ASN H3 4 20.166000366211 20.499057769775<br>> 20.535308837891 0.0000000000000 0.0000000000000 0.0000000000000<br>> 1ASN C7 5 20.295000076294 20.426000595093<br>> 20.385000228882 0.0000000000000 0.0000000000000 0.0000000000000<br>> 1ASN O1 6 20.315000534058 20.309999465942<br>> 20.349000930786 0.0000000000000 0.0000000000000 0.0000000000000<br>> 1ASN N2 7 20.393997192383 20.515981674194<br>> 20.393993377686 0.0000000000000 0.0000000000000 0.0000000000000<br>> 1ASN H4 8 20.489086151123 20.482969284058<br>> 20.386993408203 0.0000000000000 0.0000000000000 0.0000000000000<br>> 1ASN H5 9 20.374940872192 20.611291885376<br>> 20.421081542969 0.0000000000000 0.0000000000000 0.0000000000000<br>> 2SOL OW 10 20.548002243042 20.120998382568<br>> 20.291999816895 0.0000000000000 0.0000000000000 0.0000000000000<br>> 2SOL HW1 11 20.500000000000 20.046926498413<br>> 20.254966735840 0.0000000000000 0.0000000000000 0.0000000000000<br>> 2SOL HW2 12 20.479961395264 20.183086395264<br>> 20.318038940430 0.0000000000000 0.0000000000000 0.0000000000000<br>> 2SOL MW 13 20.535623550415 20.119720458984<br>> 20.290826797485 -0.0009536742582 0.0000000000000 0.0000000000000<br>> 3SOL OW 14 20.242019653320 20.178009033203<br>> 20.123998641968 0.0000000000000 0.0000000000000 0.0000000000000<br>> 3SOL HW1 15 20.164087295532 20.143032073975<br>> 20.167186737061 0.0000000000000 0.0000000000000 0.0000000000000<br>> 3SOL HW2 16 20.300615310669 20.201835632324<br>> 20.195838928223 0.0000000000000 0.0000000000000 0.0000000000000<br>> 3SOL MW 17 20.239955902100 20.176818847656<br>> 20.136268615723 -0.0085830679163 -0.0038146970328 0.0000000000000<br>> 40.642551422119 40.642551422119 40.642551422119<br>> <br>> <br>> Maybe this is just wishful thinking, but it would be nice if the<br>> manual actually explained the specifications of the gro file format.<br>> For example, it is clearly not fixed-width, as the number of digits in<br>> the columns can vary, but at the same time it doesn't appear to be<br>> tab/space delimited, as the columns of velocities can occasionally run<br>> together (if I'm using the -ndec option, especially). Obviously one<br>> can look at the code (perhaps I should do this) but it seems it should<br>> be documented.<br>> <br>> Thanks,<br>> David<br>> <br>> <br>> <br>> > If you want high precision use g96.<br>> ><br>> >><br>> >><br>> >> ------------------------------------------------------------------------<br>> >><br>> >> _______________________________________________<br>> >> gmx-users mailing list gmx-users@gromacs.org<br>> >> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> >> Please search the archive at http://www.gromacs.org/search before posting!<br>> >> Please don't post (un)subscribe requests to the list. Use the www<br>> >> interface or send it to gmx-users-request@gromacs.org.<br>> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> ><br>> ><br>> > --<br>> > David van der Spoel, Ph.D., Professor of Biology<br>> > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.<br>> > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.<br>> > spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the www interface<br>> > or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> ><br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br><hr>Express yourself instantly with MSN Messenger! <a href="http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/">MSN Messenger</a><br /><hr />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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