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On 27/11/2011 10:15 PM, Igor Druz wrote:
<blockquote
cite="mid:CAPEHq6_WppSB-rv=xrMV2ww+xB18qiOonPLrgWHCMNNW49t27Q@mail.gmail.com"
type="cite">write to gro in angstroms, read from gro in angstroms,
convert into nm in grompp.<br>
</blockquote>
<br>
What are you trying to communicate with this hypothetical workflow?<br>
<br>
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.<br>
<br>
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.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAPEHq6_WppSB-rv=xrMV2ww+xB18qiOonPLrgWHCMNNW49t27Q@mail.gmail.com"
type="cite"><br>
<div class="gmail_quote">On Sun, Nov 27, 2011 at 10:41 AM, Tsjerk
Wassenaar <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex;">Hi Igor,<br>
<br>
Please do read the manual. The GRO file format is a
fixed-width format<br>
with %8.3f for coordinates, velocities and forces. Changing
the format<br>
to %9.4f will break everything written in fortran. And, yes,
people<br>
still use fortran. So which point did I miss? :)<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<div class="HOEnZb">
<div class="h5"><br>
<br>
On Sun, Nov 27, 2011 at 11:38 AM, Igor Druz <<a
moz-do-not-send="true" href="mailto:idruz512@gmail.com">idruz512@gmail.com</a>>
wrote:<br>
> You are missing the point. Quoting my response to
David:<br>
><br>
> I appreciate the history of the matter, but it would
save a lot of headache<br>
> to store coordinates in angstroms in gro files, i.e.,
not to omit "2" in<br>
> 4.172 A in the pdb file by converting it to 0.417 nm
in the gro file. What<br>
> is the point in dropping useful "2" by introducing
useless "0"?<br>
><br>
> On Sun, Nov 27, 2011 at 10:30 AM, Tsjerk Wassenaar
<<a moz-do-not-send="true"
href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>><br>
> wrote:<br>
>><br>
>> My my. Why is it a fault to adhere to ISO units
(nm) over non-standard<br>
>> (A)? It's a choice, but a choice is not faulty.
The consequences may<br>
>> be undesirable. But shouldn't a user, certainly a
computation<br>
>> scientist, understand the file formats, as an
experimentalist should<br>
>> know its solvent? And know the consequences of
using one over another?<br>
>> Mark is correct to state that a picometer
uncertainty at the start has<br>
>> no consequences for molecular dynamics
simulations. For single point<br>
>> eneriges they will have. But no one ever forced
anyone to use GRO<br>
>> rather than PDB format. That's the choice the
researcher makes. And,<br>
>> at least in my tutorial, that difference between
GRO and PDB format is<br>
>> stressed. The choice to use standard units is
historical, and lies<br>
>> decades back in time. Could we now change it to
A, because a 'faulty'<br>
>> choice was made?<br>
>><br>
>> I'm terribly sorry that you need to do a lot of
work again, Igor. But<br>
>> you can't shove the blame in another's shoes. You
overlooked<br>
>> something, lead by presumptions about
standardization in units and<br>
>> file formats. May I wonder why you only found out
now, after all the<br>
>> work has been done? This difference would have
showed up with the<br>
>> first test, right? But again, it's not us against
you, and I'm sorry<br>
>> you have to go through this. Trust me, most of us
have had such<br>
>> moments, although with a different aspect.<br>
>><br>
>> Best,<br>
>><br>
>> Tsjerk<br>
>><br>
>> On Sun, Nov 27, 2011 at 11:03 AM, Igor Druz <<a
moz-do-not-send="true" href="mailto:idruz512@gmail.com">idruz512@gmail.com</a>>
wrote:<br>
>> > You can put whichever spin you like into
what is said, but there is a<br>
>> > clear<br>
>> > (and unnecessary) fault with the way
coordinates are stored in gro files<br>
>> > when made from pdb using pdb2gmx.<br>
>> ><br>
>> > On Sun, Nov 27, 2011 at 12:39 AM, Mark
Abraham <<a moz-do-not-send="true"
href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>><br>
>> > wrote:<br>
>> >><br>
>> >> On 27/11/2011 5:07 AM, Igor Druz wrote:<br>
>> >><br>
>> >> On Sat, Nov 26, 2011 at 5:35 PM, <<a
moz-do-not-send="true"
href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>>
wrote<br>
>> >>><br>
>> >>> 1. why repeat the calculations? If
you're talking about simulations<br>
>> >>> then<br>
>> >>> there is no need to repeat them due
to this. You will get different<br>
>> >>> answers<br>
>> >>> with the same starting coordinates
if you simply change the initial<br>
>> >>> velocities. If you're talking about
instantaneous energy calculations<br>
>> >>> then I<br>
>> >>> suppose you might need to redo it,
but they should be very quick,<br>
>> >>> right?<br>
>> >>><br>
>> >><br>
>> >> The calculations must be repeated. You
are making irrelevant<br>
>> >> assumptions<br>
>> >> without knowing what the calculations
are for.<br>
>> >><br>
>> >> You asserted that there should have been
a warning without explaining<br>
>> >> why<br>
>> >> this loss of precision was material.
Chris knew that many uses of<br>
>> >> pdb2gmx<br>
>> >> change the atomic configuration
considerably, e.g. new hydrogen<br>
>> >> positions,<br>
>> >> building termini, etc. so that any
change of precision of coordinates<br>
>> >> is not<br>
>> >> a big deal, and even less important once
a simulation has run<br>
>> >> afterwards. If<br>
>> >> you want to engage in constructive
dialogue, please explain why the<br>
>> >> loss of<br>
>> >> precision was material, in order to
clarify the reason for your request<br>
>> >> for<br>
>> >> a warning message. If you wish to blow
off steam, please do it<br>
>> >> elsewhere.<br>
>> >><br>
>> >><br>
>> >>><br>
>> >>> 2. The .gro files do not carry
useless zeroes. you have it<br>
>> >>> backwards...<br>
>> >>> the gro files end up with fewer
digits.<br>
>> >>><br>
>> >><br>
>> >> 0.417 or 4.172. Shall I continue? I know
which one I prefer.<br>
>> >><br>
>> >>><br>
>> >>> 3. it's a little annoying to find
out that you already knew the<br>
>> >>> answer.<br>
>> >>> Why not state that at the outset?
Unless I misunderstand this point,<br>
>> >>> this<br>
>> >>> will mark the end of my comments
since holding back information on<br>
>> >>> purpose<br>
>> >>> just wastes people's time.<br>
>> >>><br>
>> >><br>
>> >> Check my 1st e-mail, please. It is NOT
asking for clarification. It is<br>
>> >> requesting an explicit warning message.<br>
>> >><br>
>> >> There's nothing to warn about. You
thought that "switching from<br>
>> >> Angstrom<br>
>> >> to nanometers" was significant somehow,
and then assumed that different<br>
>> >> file<br>
>> >> formats would definitely contain
identical information, and didn't<br>
>> >> check<br>
>> >> their contents.<br>
>> >><br>
>> >> Mark<br>
>> >><br>
>> >><br>
>> >>><br>
>> >>> Chris.<br>
>> >>><br>
>> >>> -- original message --<br>
>> >>><br>
>> >>> I already knew the reason. But I had
to find this out hard way. Now<br>
>> >>> facing<br>
>> >>> a dreading prospect of repeating
tons of calculations! Hence the<br>
>> >>> request<br>
>> >>> for the "bad for the health" sign.
Btw, gromacs issues a lot of<br>
>> >>> warnings,<br>
>> >>> but not this one :D<br>
>> >>><br>
>> >>> What a bright idea to switch from
angstroms to nanometers! Now the gro<br>
>> >>> files carry a lot of useless zeros.<br>
>> >>><br>
>> >>><br>
>> >>> --<br>
>> >>> gmx-users mailing list <a
moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
>> >>> <a moz-do-not-send="true"
href="http://lists.gromacs.org/mailman/listinfo/gmx-users"
target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a>
before posting!<br>
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>> >><br>
>> >><br>
>> >><br>
>> >> --<br>
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>> ><br>
>> ><br>
>> > --<br>
>> > gmx-users mailing list <a
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>> > <a moz-do-not-send="true"
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before posting!<br>
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>> ><br>
>><br>
>><br>
>><br>
>> --<br>
>> Tsjerk A. Wassenaar, Ph.D.<br>
>><br>
>> post-doctoral researcher<br>
>> Molecular Dynamics Group<br>
>> * Groningen Institute for Biomolecular Research
and Biotechnology<br>
>> * Zernike Institute for Advanced Materials<br>
>> University of Groningen<br>
>> The Netherlands<br>
>> --<br>
>> gmx-users mailing list <a
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><br>
><br>
> --<br>
> gmx-users mailing list <a moz-do-not-send="true"
href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>
> <a moz-do-not-send="true"
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before posting!<br>
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><br>
<br>
<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and
Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
--<br>
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before posting!<br>
Please don't post (un)subscribe requests to the list. Use
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