[gmx-users] multple 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:
>
> Fatal error:Atom 3176 in multple T-coupling groups(13 and 1)
>
> Where the atom 3176 corresponds to the last atom of the ligand.
>
> I check up the mailing list and know that i have some error in my .mdp
> file.
> But i don`t know how can i fix it.
>
> The tail of .top is :
> ; Compound        #mols
> Protein_A           1
> Protein_B           1
> Protein_C           1
> Protein_D           1
> SOL               143
> SOL             4318

Add both SOL groups here ( SOL 143+4318)

>
> The contents of .mdp is :
> [ molecules ]
> ; Compound        #mols
> Protein_A           1
> Protein_B           1
> Protein_C           1
> Protein_D           1
> SOL               143
> SOL             4318
> [root at dhcp040 ~]# cat PR.mdp
> title               =  PR
> warnings            =  10
> cpp                 =  /lib/cpp
> define              =  -DPOSRES
> constraints         =  all-bonds
> integrator          =  md
> dt                  =  0.001    ; ps !
> nsteps              =  1000     ; total 1.0 ps.
> nstcomm             =  1
> nstxout             =  10
> nstvout             =  100
> nstfout             =  0
> nstlog              =  100
> nstenergy           =  100
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.0
> rcoulomb            =  1.0
> rvdw                =  1.0
> ; Berendsen temperature coupling is on in two groups
> Tcoupl              =  berendsen
> tau_t               =  0.1              0.1             0.1
> tc-grps             =  protein          sol             sol
> ref_t               =  300              300             300

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.

> ; Pressure coupling is not on
> Pcoupl              =  no
> tau_p               =  0.5
> compressibility     =  4.5e-5
> ref_p               =  1.0
> ; Generate velocites is on at 300 K.
> gen_vel             =  yes
> gen_temp            =  300.0
> gen_seed            =  173529
>


Greetings,

Florian

------------------------------------------------------------------------
 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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