On Sat, Nov 26, 2011 at 6:37 PM, David van der Spoel <sp...@xray.bmc.uu.se>wrote:
> On 2011-11-26 19:07, Igor Druz wrote: > >> On Sat, Nov 26, 2011 at 5:35 PM, <chris.ne...@utoronto.ca >> <mailto:chris.neale@utoronto.**ca <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. >> >> 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. >> > > You have the option to use pdb or gro or g96. The last format has even > more digits, and support for velocities. Pdb has no velocities and gro has > lowest precision. > All of these are file formats that have not been developed by the gromacs > team, but were adopted from other packages. I don't see what kind of > warning we should issue when using a gro file, without making it even more > confusing. > it was already in your 1st response: the gro has less decimal digits than pdb when storing coordinates. This should be issued by pdb2gmx. 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"? > >> 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 >> <mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/__**mailman/listinfo/gmx-users<http://lists.gromacs.org/__mailman/listinfo/gmx-users> >> >> >> <http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >> > >> Please search the archive at >> >> http://www.gromacs.org/__**Support/Mailing_Lists/Search<http://www.gromacs.org/__Support/Mailing_Lists/Search> >> >> >> <http://www.gromacs.org/**Support/Mailing_Lists/Search<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 >> <mailto:gmx-users-request@**gromacs.org<gmx-users-requ...@gromacs.org> >> >. >> Can't post? Read >> http://www.gromacs.org/__**Support/Mailing_Lists<http://www.gromacs.org/__Support/Mailing_Lists> >> >> <http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >> > >> >> >> >> >> > > -- > David van der Spoel, Ph.D., Professor of Biology > Dept. of Cell & Molec. Biol., Uppsala University. > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > sp...@xray.bmc.uu.se http://folding.bmc.uu.se > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<http://www.gromacs.org/Support/Mailing_Lists> >
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