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 >
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