[gmx-users] Restraints for specific residues

Mark Abraham Mark.Abraham at anu.edu.au
Tue Jan 31 09:20:15 CET 2012

On 31/01/2012 7:14 PM, Андрей Гончар wrote:
> So for every residue I need to specify their atoms, am I right?

Yeah. One way is to use make_ndx to select the atoms in the residues and 
make an index file group, then genrestr, then #include the generated 
.itp file.


> 2012/1/31 Mark Abraham<Mark.Abraham at anu.edu.au>:
>> On 31/01/2012 7:06 PM, Андрей Гончар wrote:
>>> Hi!
>>> Is it possible to specify which residues to restrain during MD simulation?
>>> For example I have a protein, but I don't want to restrain all the
>>> molecule, but a part.
>>> How can I do this?
>> See http://www.gromacs.org/Documentation/How-tos/Position_Restraints. You
>> need to choose the atoms and create a suitable [position_restraints]
>> section.
>> Mark
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