On Sun, Nov 27, 2011 at 11:26 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote:
> On 27/11/2011 10:15 PM, Igor Druz wrote: > > write to gro in angstroms, read from gro in angstroms, convert into nm in > grompp. > > > What are you trying to communicate with this hypothetical workflow? > > Historical file formats imply particular units and are often limited to a > particular precision. Nothing should or will be done to change this. > Eventually file formats will be flexible enough to specify arbitrary > precision in arbitrary units, but that day is not here yet. Even when we > get there, workmen will still have to know about their tools work in order > to use them. > > I still haven't seen any evidence beyond Igor's assertion that there's a > problem worth a warning, so I'm going to regard that issue as closed. > > Mark > > > > On Sun, Nov 27, 2011 at 10:41 AM, Tsjerk Wassenaar <tsje...@gmail.com>wrote: > >> 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 >> >> Back to square one! The point you are missing is that 4.172 A is not equal to 0.417 nm and pdb2gmx does it without any warning. >> 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 >> > > > > > > -- > 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 >
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