On Sat, Nov 26, 2011 at 6:37 PM, David van der Spoel <span dir="ltr"><<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>></span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<div class="im">On 2011-11-26 19:07, Igor Druz wrote:<br>
</div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">
On Sat, Nov 26, 2011 at 5:35 PM, <<a href="mailto:chris.neale@utoronto.ca" target="_blank">chris.neale@utoronto.ca</a><br></div>
<mailto:<a href="mailto:chris.neale@utoronto.ca" target="_blank">chris.neale@utoronto.<u></u>ca</a>>> wrote<div class="im"><br>
<br>
1. why repeat the calculations? If you're talking about simulations<br>
then there is no need to repeat them due to this. You will get<br>
different answers with the same starting coordinates if you simply<br>
change the initial velocities. If you're talking about instantaneous<br>
energy calculations then I suppose you might need to redo it, but<br>
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>
2. The .gro files do not carry useless zeroes. you have it<br>
backwards... 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>
3. it's a little annoying to find out that you already knew the<br>
answer. Why not state that at the outset? Unless I misunderstand<br>
this point, this will mark the end of my comments since holding back<br>
information on purpose 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>
</div></blockquote>
<br>
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. <br></blockquote><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
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.<br>
</blockquote><div><br>it was already in your 1st response: the gro has less decimal digits than pdb when storing coordinates. This should be issued by pdb2gmx.<br><br>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"?<br><br></div><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">
<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>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
<a href="http://lists.gromacs.org/__mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/__<u></u>mailman/listinfo/gmx-users</a><div class="im"><br>
<<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>mailman/listinfo/gmx-users</a>><br>
Please search the archive at<br></div>
<a href="http://www.gromacs.org/__Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/__<u></u>Support/Mailing_Lists/Search</a><div class="im"><br>
<<a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists/Search</a>> before posting!<br>
Please don't post (un)subscribe requests to the list. Use thewww<br>
interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a><br></div>
<mailto:<a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@<u></u>gromacs.org</a>>.<br>
Can't post? Read <a href="http://www.gromacs.org/__Support/Mailing_Lists" target="_blank">http://www.gromacs.org/__<u></u>Support/Mailing_Lists</a><br>
<<a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a>><br>
<br>
<br>
<br>
<br>
</blockquote>
<br>
<br>
-- <br>
David van der Spoel, Ph.D., Professor of Biology<br>
Dept. of Cell & Molec. Biol., Uppsala University.<br>
Box 596, 75124 Uppsala, Sweden. Phone: <a href="tel:%2B46184714205" value="+46184714205" target="_blank">+46184714205</a>.<br>
<a href="mailto:spoel@xray.bmc.uu.se" target="_blank">spoel@xray.bmc.uu.se</a> <a href="http://folding.bmc.uu.se" target="_blank">http://folding.bmc.uu.se</a><div class="im"><br>
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/<u></u>mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists/Search</a> before posting!<br></div>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<div class="HOEnZb"><div class="h5">
<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/<u></u>Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br>