[gmx-users] genion error

[Yang Ye]

fatal error may be not caused by Na+ in the simulation. perhaps the way 
you hv put them with genion, or the system you have.
Also, a loose coupling at t_tau = 0.5 could be just enough.

Bharat V. Adkar P.hD Student wrote:
> 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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-- 
/Regards,/
Yang Ye
/Computational Biology Lab
School of Biological Sciences
Nanyang Technological University
Singapore
Tel: 6316-2884
/