[gmx-users] equilibration

[Anton Feenstra]

Xavier Periole wrote:
>>A question that will be a problem later: I would like to scale the
>>temperature of the peptide, the lipids and water+ions separately. How
>>should I formulate this in the .mdp file? (How to put water and ions in
>>the same group?)
>>-------------------
>>tcoupl  = Berendsen
>>tc_grps = Protein DPPC (SOL Cl)   ?????
>>tau_t   =   0.1    0.1   0.1
>>ref_t   =    30     30    30
>>----------------------------
>>
> 
> 
> sounds good.

But isn't. You can't use brackets () in your .mdp file. You should create
a combined SOL+Cl index group first, using e.g. make_ndx (or a text editor).
Then, your .mdp file line would read:
tc_grps = Protein DPPC SOL+Cl

Where 'SOL+Cl' is the name of your combined Solvent and ions group, obviously.

> 
> 
>>The topology file looks like this (Note that in the [molecules] section
>>I have commented away the "Protein 1" line. If I keep thath line, grompp
>>complains and count the number of atoms in the protein twice!!?? The
>>rw-conn.itp file describes the peptide.):
[...]
>>[ molecules ]
>>; name number
>>;Protein 1
>>DPPC 64
>>SOL 2463
>>Cl 3
>>
> 
> Looks like there is a problem in the definition of your system. In your pdb
> or gro file is the order of appeareance protein, dppc, sol and CL ? That
> could be a conflict.

Is there already a [system]+[molecules] section in your rw-conn.itp? You
probably should remove that, and keep the line 'Protein 1' in your .top
file, to avoid confusion here. An .itp file for a molecule (peptide, protein,
lipid, whatever), should normally only contain [atoms], [bonds], [pairs],
[angles], [dihedrals] and [exclusions].


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |
|_____________|_______________________________________________________|