On 2011-11-26 20:15, Igor Druz wrote:
On Sat, Nov 26, 2011 at 6:37 PM, David van der Spoel
<sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>> wrote:
On 2011-11-26 19:07, Igor Druz wrote:
On Sat, Nov 26, 2011 at 5:35 PM, <chris.ne...@utoronto.ca
<mailto:chris.ne...@utoronto.ca>
<mailto:chris.neale@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.
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.
You have the option to use pdb or gro or g96. The last format has
even more digits, and support for velocities. Pdb has no velocities
and gro has lowest precision.
All of these are file formats that have not been developed by the
gromacs team, but were adopted from other packages. I don't see what
kind of warning we should issue when using a gro file, without
making it even more confusing.
it was already in your 1st response: the gro has less decimal digits
than pdb when storing coordinates. This should be issued by pdb2gmx.
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"?
History as well. You can have pdb2gmx go straight to g96 (-c conf.g96
will do it) which has higher precision than either of the two others. It
is bigger though.
As said g96 is also a borrowed format from gromos96.
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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