[gmx-users] to gro or not to gro

Sun Nov 27 11:38:11 CET 2011

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 <tsjerkw at 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 <idruz512 at 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.Abraham at anu.edu.au>
> > wrote:
> >>
> >> On 27/11/2011 5:07 AM, Igor Druz wrote:
> >>
> >> On Sat, Nov 26, 2011 at 5:35 PM, <chris.neale at 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.
> >>>
> >>>
> >>> --
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> >>
> >>
> >>
> >>
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>
>
> --
> 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
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