[gmx-users] to gro or not to gro

Mark Abraham Mark.Abraham at anu.edu.au
Sun Nov 27 01:39:27 CET 2011

On 27/11/2011 5:07 AM, 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.

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.


>     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.
>     -- 
>     gmx-users mailing list gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>     Please don't post (un)subscribe requests to the list. Use thewww
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111127/f8957958/attachment.html>

More information about the gromacs.org_gmx-users mailing list