write to gro in angstroms, read from gro in angstroms, convert into nm in grompp.
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 > > > 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
