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On 27/11/2011 5:07 AM, Igor Druz wrote:
<blockquote
cite="mid:CAPEHq6_oa1B-KCaBmNDtmMQ32Vx2-omduNr9D=_YSib332n-aw@mail.gmail.com"
type="cite">On Sat, Nov 26, 2011 at 5:35 PM, <span dir="ltr"><<a
moz-do-not-send="true" href="mailto:chris.neale@utoronto.ca">chris.neale@utoronto.ca</a>></span>
wrote<br>
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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?<br>
<br>
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<div>The calculations must be repeated. You are making
irrelevant assumptions without knowing what the calculations
are for.</div>
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<br>
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.<br>
<br>
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cite="mid:CAPEHq6_oa1B-KCaBmNDtmMQ32Vx2-omduNr9D=_YSib332n-aw@mail.gmail.com"
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2. The .gro files do not carry useless zeroes. you have it
backwards... the gro files end up with fewer digits.<br>
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<div>0.417 or 4.172. Shall I continue? I know which one I
prefer.</div>
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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.<br>
<br>
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<div>Check my 1st e-mail, please. It is NOT asking for
clarification. It is requesting an explicit warning message.</div>
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<br>
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.<br>
<br>
Mark<br>
<br>
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cite="mid:CAPEHq6_oa1B-KCaBmNDtmMQ32Vx2-omduNr9D=_YSib332n-aw@mail.gmail.com"
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Chris.<br>
<br>
-- original message --<br>
<br>
I already knew the reason. But I had to find this out hard
way. Now 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.<span class="HOEnZb"><font
color="#888888"><br>
<br>
<br>
-- <br>
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