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

Yunhong Hotta 4yunhong at bunshi3.bio.nagoya-u.ac.jp
Thu Feb 24 09:06:17 CET 2005

Hi all

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

Could anyone be so kind to tell me how to fix this error?

Thank for your time !


Yunhong Hotta ( Research Assitant )
email : 4yunhong at bunshi3.bio.naogya-u.ac.jp
Division of biological science
Graduate School of Science
Nogoya University 

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