[gmx-users] genion error

[Hiromichi Tsurui]

Thank you Yang Ye;

As I wrote to Bharat, I changed tc-gps of mdp file from "protein SOL" to 
"protein other".
Then grompp worked well and I could run mdrun.

Thank you.

Hiromichi
----- Original Message ----- 
From: "Yang Ye" <leafyoung81-group at yahoo.com>
To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
Sent: Thursday, January 19, 2006 6:36 PM
Subject: Re: [gmx-users] genion error


> 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
>>>>> _______________________________________________
>>>>> gmx-users mailing list
>>>>> gmx-users at gromacs.org
>>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>>>> Please don't post (un)subscribe requests to the list. Use the www 
>>>>> interface or send it to gmx-users-request at gromacs.org.
>>>>>
>>>>
>>>> -- 
>>>> /Regards,/
>>>> Yang Ye
>>>> /Computational Biology Lab
>>>> School of Biological Sciences
>>>> Nanyang Technological University
>>>> Singapore
>>>> Tel: 6316-2884
>>>> /
>>>> _______________________________________________
>>>> gmx-users mailing list
>>>> gmx-users at gromacs.org
>>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>>> Please don't post (un)subscribe requests to the list. Use the www 
>>>> interface or send it to gmx-users-request at gromacs.org.
>>>>
>>>>
>>>
>>> _______________________________________________
>>> gmx-users mailing list
>>> gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please don't post (un)subscribe requests to the list. Use the www 
>>> interface or send it to gmx-users-request at gromacs.org.
>>>
>> _______________________________________________
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the www 
>> interface or send it to gmx-users-request at gromacs.org.
>>
>
> -- 
> /Regards,/
> Yang Ye
> /Computational Biology Lab
> School of Biological Sciences
> Nanyang Technological University
> Singapore
> Tel: 6316-2884
> /
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.
>
>