feenstra at chem.vu.nl
Tue Aug 12 09:01:03 CEST 2003
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
> 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].
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
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| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
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