[gmx-users] to gro or not to gro

Sun Nov 27 12:15:41 CET 2011

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 <tsjerkw at 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 <idruz512 at 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 <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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> >
> >
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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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