[gmx-users] to gro or not to gro

Sun Nov 27 11:41:22 CET 2011

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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-- 
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