On 27/11/2011 5:07 AM, Igor Druz wrote:
On Sat, Nov 26, 2011 at 5:35 PM, <chris.ne...@utoronto.ca
<mailto:chris.ne...@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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