[gmx-users] again the multiple T-coupling errors

[Haberl Florian]

Hi

>
> I just run the MD run of a protein without deleting the crystallographic
> water. When i go for grompp with positional restraint, I get an fatal
> error  as:Atom 3176 in multple T-coupling groups(13 and 1)
>
> I got Florian`s advice in gmx-users Digest Vol 10 Issuse 35 and did what
> he said .
> I thank Florian so much at the first, but I still can`t fix the problem
> .
>
>>Add both SOL groups here ( SOL 143+4318)
>
> I did as :
>
> Protein_A           1
> Protein_B           1
> Protein_C           1
> Protein_D           1
> SOL              4461
>
>>add here your PROTEIN_{A,D} and erease second sol grp.
>>For each defined group in your top file you need one in your
>>temperature coupling.
>
> So I edit the .mdp as :
>
> Tcoupl              =  berendsen
> tau_t               =  0.1              0.1             0.1
> 0.1             0.1
> tc-grps             =  Protein_A        Protein_B       Protein_C
> Protein_D       sol
> ref_t               =  300              300             300
> 300             300
> ; Pressure coupling is not on
>
> But when I run grompp again , the program told me
> " Group Protein_A not found in indexfile " and stopped.
>
> I want to check the index file. but I don`t know which is the index
> file.
>
> Could anyone be so kind to tell me how to fix this error?

take a look at your itp and top files (depends on how you add them), in
there you should also have the correct names so it have to be there
"Protein_{A,D}".

Also i would rise tau_t to 1.0 .


Greetings,

Florian


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 Florian Haberl              Universitaet Erlangen/Nuernberg
 Computer-Chemie-Centrum     Naegelsbachstr. 25, D-91052 Erlangen

 Mailto: florian.haberl AT chemie.uni-erlangen.de

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