[gmx-users] to gro or not to gro

[Igor Druz]

On Sat, Nov 26, 2011 at 6:37 PM, David van der Spoel
<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 <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"?


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