Hi Igor, Please do read the manual. The GRO file format is a fixed-width format with %8.3f for coordinates, velocities and forces. Changing the format to %9.4f will break everything written in fortran. And, yes, people still use fortran. So which point did I miss? :)
Cheers, Tsjerk On Sun, Nov 27, 2011 at 11:38 AM, Igor Druz <idruz...@gmail.com> wrote: > You are missing the point. Quoting my response to David: > > I appreciate the history of the matter, but it would save a lot of headache > to store coordinates in angstroms in gro files, i.e., not to omit "2" in > 4.172 A in the pdb file by converting it to 0.417 nm in the gro file. What > is the point in dropping useful "2" by introducing useless "0"? > > On Sun, Nov 27, 2011 at 10:30 AM, Tsjerk Wassenaar <tsje...@gmail.com> > wrote: >> >> My my. Why is it a fault to adhere to ISO units (nm) over non-standard >> (A)? It's a choice, but a choice is not faulty. The consequences may >> be undesirable. But shouldn't a user, certainly a computation >> scientist, understand the file formats, as an experimentalist should >> know its solvent? And know the consequences of using one over another? >> Mark is correct to state that a picometer uncertainty at the start has >> no consequences for molecular dynamics simulations. For single point >> eneriges they will have. But no one ever forced anyone to use GRO >> rather than PDB format. That's the choice the researcher makes. And, >> at least in my tutorial, that difference between GRO and PDB format is >> stressed. The choice to use standard units is historical, and lies >> decades back in time. Could we now change it to A, because a 'faulty' >> choice was made? >> >> I'm terribly sorry that you need to do a lot of work again, Igor. But >> you can't shove the blame in another's shoes. You overlooked >> something, lead by presumptions about standardization in units and >> file formats. May I wonder why you only found out now, after all the >> work has been done? This difference would have showed up with the >> first test, right? But again, it's not us against you, and I'm sorry >> you have to go through this. Trust me, most of us have had such >> moments, although with a different aspect. >> >> Best, >> >> Tsjerk >> >> On Sun, Nov 27, 2011 at 11:03 AM, Igor Druz <idruz...@gmail.com> wrote: >> > You can put whichever spin you like into what is said, but there is a >> > clear >> > (and unnecessary) fault with the way coordinates are stored in gro files >> > when made from pdb using pdb2gmx. >> > >> > On Sun, Nov 27, 2011 at 12:39 AM, Mark Abraham <mark.abra...@anu.edu.au> >> > wrote: >> >> >> >> On 27/11/2011 5:07 AM, Igor Druz wrote: >> >> >> >> On Sat, Nov 26, 2011 at 5:35 PM, <chris.ne...@utoronto.ca> wrote >> >>> >> >>> 1. why repeat the calculations? If you're talking about simulations >> >>> then >> >>> there is no need to repeat them due to this. You will get different >> >>> answers >> >>> with the same starting coordinates if you simply change the initial >> >>> velocities. If you're talking about instantaneous energy calculations >> >>> then I >> >>> suppose you might need to redo it, but they should be very quick, >> >>> right? >> >>> >> >> >> >> The calculations must be repeated. You are making irrelevant >> >> assumptions >> >> without knowing what the calculations are for. >> >> >> >> You asserted that there should have been a warning without explaining >> >> why >> >> this loss of precision was material. Chris knew that many uses of >> >> pdb2gmx >> >> change the atomic configuration considerably, e.g. new hydrogen >> >> positions, >> >> building termini, etc. so that any change of precision of coordinates >> >> is not >> >> a big deal, and even less important once a simulation has run >> >> afterwards. If >> >> you want to engage in constructive dialogue, please explain why the >> >> loss of >> >> precision was material, in order to clarify the reason for your request >> >> for >> >> a warning message. If you wish to blow off steam, please do it >> >> elsewhere. >> >> >> >> >> >>> >> >>> 2. The .gro files do not carry useless zeroes. you have it >> >>> backwards... >> >>> the gro files end up with fewer digits. >> >>> >> >> >> >> 0.417 or 4.172. Shall I continue? I know which one I prefer. >> >> >> >>> >> >>> 3. it's a little annoying to find out that you already knew the >> >>> answer. >> >>> Why not state that at the outset? Unless I misunderstand this point, >> >>> this >> >>> will mark the end of my comments since holding back information on >> >>> purpose >> >>> just wastes people's time. >> >>> >> >> >> >> Check my 1st e-mail, please. It is NOT asking for clarification. It is >> >> requesting an explicit warning message. >> >> >> >> There's nothing to warn about. You thought that "switching from >> >> Angstrom >> >> to nanometers" was significant somehow, and then assumed that different >> >> file >> >> formats would definitely contain identical information, and didn't >> >> check >> >> their contents. >> >> >> >> Mark >> >> >> >> >> >>> >> >>> Chris. >> >>> >> >>> -- original message -- >> >>> >> >>> I already knew the reason. But I had to find this out hard way. Now >> >>> facing >> >>> a dreading prospect of repeating tons of calculations! Hence the >> >>> request >> >>> for the "bad for the health" sign. Btw, gromacs issues a lot of >> >>> warnings, >> >>> but not this one :D >> >>> >> >>> What a bright idea to switch from angstroms to nanometers! Now the gro >> >>> files carry a lot of useless zeros. >> >>> >> >>> >> >>> -- >> >>> gmx-users mailing list gmx-users@gromacs.org >> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >> >>> Please search the archive at >> >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> >>> Please don't post (un)subscribe requests to the list. Use thewww >> >>> interface or send it to gmx-users-requ...@gromacs.org. >> >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> gmx-users mailing list gmx-users@gromacs.org >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> >> Please search the archive at >> >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >> > >> > >> > -- >> > gmx-users mailing list gmx-users@gromacs.org >> > http://lists.gromacs.org/mailman/listinfo/gmx-users >> > Please search the archive at >> > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >> > >> >> >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> >> post-doctoral researcher >> Molecular Dynamics Group >> * Groningen Institute for Biomolecular Research and Biotechnology >> * Zernike Institute for Advanced Materials >> University of Groningen >> The Netherlands >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
