You are missing the point. Quoting my response to David:<div><br></div><div><pre style="background-color: rgb(255, 255, 255); -webkit-text-stroke-color: initial !important; background-image: none !important; ">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"?</pre><br><div class="gmail_quote">On Sun, Nov 27, 2011 at 10:30 AM, Tsjerk Wassenaar <span dir="ltr"><<a 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;">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>
<div class="HOEnZb"><div class="h5"><br>
On Sun, Nov 27, 2011 at 11:03 AM, Igor Druz <<a 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 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 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 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 then<br>
>>> there is no need to repeat them due to this. You will get different answers<br>
>>> with the same starting coordinates if you simply change the initial<br>
>>> velocities. If you're talking about instantaneous energy calculations then I<br>
>>> suppose you might need to redo it, but they should be very quick, right?<br>
>>><br>
>><br>
>> The calculations must be repeated. You are making irrelevant assumptions<br>
>> without knowing what the calculations are for.<br>
>><br>
>> You asserted that there should have been a warning without explaining why<br>
>> this loss of precision was material. Chris knew that many uses of pdb2gmx<br>
>> change the atomic configuration considerably, e.g. new hydrogen positions,<br>
>> building termini, etc. so that any change of precision of coordinates is not<br>
>> a big deal, and even less important once a simulation has run afterwards. If<br>
>> you want to engage in constructive dialogue, please explain why the loss of<br>
>> precision was material, in order to clarify the reason for your request for<br>
>> a warning message. If you wish to blow off steam, please do it elsewhere.<br>
>><br>
>><br>
>>><br>
>>> 2. The .gro files do not carry useless zeroes. you have it 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 answer.<br>
>>> Why not state that at the outset? Unless I misunderstand this point, this<br>
>>> will mark the end of my comments since holding back information on 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 Angstrom<br>
>> to nanometers" was significant somehow, and then assumed that different file<br>
>> formats would definitely contain identical information, and didn't 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 request<br>
>>> for the "bad for the health" sign. Btw, gromacs issues a lot of 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>
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>><br>
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>><br>
>><br>
>><br>
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<br>
<br>
<br>
</div></div><span class="HOEnZb"><font color="#888888">--<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>
</font></span><div class="HOEnZb"><div class="h5">--<br>
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