write to gro in angstroms, read from gro in angstroms, convert into nm in grompp.<br><br><div class="gmail_quote">On Sun, Nov 27, 2011 at 10:41 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;">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 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 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 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 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<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>
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>><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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><br>
><br>
> --<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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</div></div></blockquote></div><br>