[gmx-users] about T-Coupling groups

[Yang Ye]

Hi,

Use make_ndx you will see the default grouping of atoms. Type 'q' to
quit and save the index.ndx.

Those 149 atoms shall be from residue name that is unknown to Gromacs,
find it from their index number from index.ndx and add to aminoacid.dat
(increment the number on top as well) located at top directory of Gromacs.

Besides, coupling ions alone is not encourage. There were
too many times mentioning this on the list. Merge them into SOL group.

Regards,
Yang Ye

On 4/23/2007 10:23 PM, Rui Li wrote:
> But in the [molecules] entry of my top file, there are only  "Protein   SOL   Cl"
> I don't know  why the 149 atoms are not included. 
> How I check them?
> Thanks in advance!
>
>
> 在您的来信中曾经提到:
>   
>> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>> Reply-To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Subject: Re: [gmx-users] about T-Coupling groups
>> Date:Mon, 23 Apr 2007 22:30:26 +1000
>>
>> Rui Li wrote:
>>     
>>> Dear all,
>>> I want run a Position-restrained dynamics simulation for my system
>>> and I write a pr.mdp file.
>>>
>>> below is part of the mdp file:
>>>
>>> Berendsen temperature coupling is on in three groups
>>> Tcoupl              =  berendsen
>>> tau_t               =  0.1       0.1     0.1
>>> tc-grps             =  Protein   SOL     Cl
>>> ref_t               =  300       300     300
>>>       
>> We discussed why this was a bad idea just last week.
>>
>>     
>>> When I use grompp, it warns:
>>>
>>> Fatal error:
>>> 149 atoms are not part of any of the T-Coupling groups
>>>
>>> what's wrong with it?
>>>       
>> You have 149 atoms that are not in Protein, SOL or Cl. All atoms must be 
>> T-coupled if any atoms are T-coupled.
>>
>> Mark
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>>     
>
>
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