[gmx-users] genion error

Bharat V. Adkar P.hD Student bharat at sscu.iisc.ernet.in
Wed Jan 18 09:28:24 CET 2006


hi Hiromichi,
whether u got the following error?
    Fatal error: Group rest not found in indexfile
if yes, you just check your mdp file for tc-grps.. if it is something 
like...
    tc-grps  = protein rest
just change the "rest" to "other", as "other" is one of the default groups 
GROMACS generates for atoms other than protein, and not the "rest". it has 
nothing to do with Na+

i think, this will help

bharat


On Wed, 18 Jan 2006, Hiromichi Tsurui wrote:

> Thank you Yang Ye;
>
> So, what values are appropriate for my system.
>
> The value ref_t        = 300 300
> tau_t       =   0.1  0.1
> caused fatal error.
> I think addition of Na+ ion is the reason of error.
>
> Thank you.
>
> Hiromichi Tsurui
>
>
> ----- Original Message ----- From: "Yang Ye" <leafyoung81-group at yahoo.com>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Sent: Monday, January 16, 2006 9:15 PM
> Subject: Re: [gmx-users] genion error
>
>
>> As a repeating theme of this list, again, it is not recommended to only 
>> couple a few atoms. Just use two groups: Protein and Rest for t-coupling.
>> 
>> bharat at sscu.iisc.ernet.in wrote:
>>>> Please let me know what values of ref_t and tau_t is appropriate for
>>>> this calculation. And any other points to correct.
>>> 
>>> i think, u have to use one more column telling ref_t and tau_t for ions, 
>>> as shown below
>>> 
>>> ref_t               =3D  300 300 300
>>> tau_t               =3D  0.1 0.1 0.1
>>> 
>>> 
>>> bharat
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>> 
>> -- 
>> /Regards,/
>> Yang Ye
>> /Computational Biology Lab
>> School of Biological Sciences
>> Nanyang Technological University
>> Singapore
>> Tel: 6316-2884
>> /
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>
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