[gmx-users] Saving trajectories of a particular group within the system

[van Bemmelen]

Hi Tsjerk,

So the claim in the online manual (under
http://www.gromacs.org/documentation/reference_3.3/online/mdp_opt.html#g
eneral), that "the difference between a dash and an underscore is
ignored", is incorrect according to you? Or is it only incorrect for the
option "xtc-groups"?

If incorrect I'd say this should be changed asap. But actually I believe
it is correct, at least for the options I've tried.

Thanks,
Jeroen



>Date: Tue, 23 Dec 2008 11:53:24 +0100
>From: "Tsjerk Wassenaar" <tsjerkw at gmail.com>
>Subject: Re: [gmx-users] Saving trajectories of a particular group
>	within the	system
>To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>Message-ID:
>	<8ff898150812230253q3e1c4267te672a59a44948d0a at mail.gmail.com>
>Content-Type: text/plain; charset=ISO-8859-1
>
>Hi Wade,
>
>>
>> I intend to generate only the trajectories of my protein alone, 
>> without outputing trajectories of the solvents. This is since the 
>> output files can get really massive. So looking at the manual, I've 
>> inserted the line: "xtc_grps = Proteins" into the .mdp input 
>file and 
>> did a short simulation to try it out.
>>
>
>"Proteins" is not a standard group, but from the paste of your 
>.mdp file it seems you used "Protein" instead, which is 
>correct. Please try to stick to literal representations.
>The real problem seems to be that "xtc_grps" is not correct, 
>but should be replaced with "xtc-grps". This almost brought me 
>to shouting "RTFM",  but a quick glance showed that the manual 
>disagrees with the source code at this point (both for 3.3.1 
>and 4.0.2). So, not your fault, really, but the correct line 
>should read
>
>xtc-grps = Protein
>
>Cheers,
>
>Tsjerk