[gmx-users] to gro or not to gro

[David van der Spoel]

On 2011-11-26 20:15, Igor Druz wrote:
> On Sat, Nov 26, 2011 at 6:37 PM, David van der Spoel
> <spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>> wrote:
>
>     On 2011-11-26 19:07, Igor Druz wrote:
>
>         On Sat, Nov 26, 2011 at 5:35 PM, <chris.neale at utoronto.ca
>         <mailto:chris.neale at utoronto.ca>
>         <mailto:chris.neale at utoronto.__ca
>         <mailto:chris.neale at 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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>     --
>     David van der Spoel, Ph.D., Professor of Biology
>     Dept. of Cell & Molec. Biol., Uppsala University.
>     Box 596, 75124 Uppsala, Sweden. Phone: +46184714205
>     <tel:%2B46184714205>.
>     spoel at xray.bmc.uu.se <mailto:spoel at xray.bmc.uu.se>
>     http://folding.bmc.uu.se
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-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se