[gmx-users] to gro or not to gro

David van der Spoel spoel at xray.bmc.uu.se
Sat Nov 26 19:37:21 CET 2011

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>> 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.

>     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.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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