[gmx-users] to gro or not to gro

[Igor Druz]

You can put whichever spin you like into what is said, but there is a clear
(and unnecessary) fault with the way coordinates are stored in gro files
when made from pdb using pdb2gmx.

On Sun, Nov 27, 2011 at 12:39 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  On 27/11/2011 5:07 AM, Igor Druz wrote:
>
> On Sat, Nov 26, 2011 at 5:35 PM, <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.
>
>
> You asserted that there should have been a warning without explaining why
> this loss of precision was material. Chris knew that many uses of pdb2gmx
> change the atomic configuration considerably, e.g. new hydrogen positions,
> building termini, etc. so that any change of precision of coordinates is
> not a big deal, and even less important once a simulation has run
> afterwards. If you want to engage in constructive dialogue, please explain
> why the loss of precision was material, in order to clarify the reason for
> your request for a warning message. If you wish to blow off steam, please
> do it elsewhere.
>
>
>
>
>> 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.
>
>
> There's nothing to warn about. You thought that "switching from Angstrom
> to nanometers" was significant somehow, and then assumed that different
> file formats would definitely contain identical information, and didn't
> check their contents.
>
> Mark
>
>
>
>
>> 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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>
>
>
>
>
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