[gmx-users] genion error
Yang Ye
leafyoung81-group at yahoo.com
Thu Jan 19 10:36:53 CET 2006
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
/
More information about the gromacs.org_gmx-users
mailing list