[gmx-users] to gro or not to gro

[Igor Druz]

On Sun, Nov 27, 2011 at 11:26 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  On 27/11/2011 10:15 PM, Igor Druz wrote:
>
> write to gro in angstroms, read from gro in angstroms, convert into nm in
> grompp.
>
>
> What are you trying to communicate with this hypothetical workflow?
>
> Historical file formats imply particular units and are often limited to a
> particular precision. Nothing should or will be done to change this.
> Eventually file formats will be flexible enough to specify arbitrary
> precision in arbitrary units, but that day is not here yet. Even when we
> get there, workmen will still have to know about their tools work in order
> to use them.
>
> I still haven't seen any evidence beyond Igor's assertion that there's a
> problem worth a warning, so I'm going to regard that issue as closed.
>
> Mark
>
>
>
> 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
>>
>> Back to square one! The point you are missing is that 4.172 A is not
equal to 0.417 nm and  pdb2gmx does it without any warning.


>> 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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>>
>>
>>
>> --
>> 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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