just make an index file (make_ndx) custom-defining the groups which you need to freeze, in your case the C-alpha of residues 18-42. Remember that, when you define new groups, you should delete the corresponding atoms from the group that contains all the rest of the protein atoms, if not you'll get an error saying that a particular atom belongs simultaneously to different freezing groups.
Hope it helps,
greetings,
MGiò
On 6/7/06, Marcelo Fabricio Masman <[EMAIL PROTECTED]> wrote:
Hi all!!!I am trying to run a MD simulation with part of my system frozen. I was looking into the manual but I couldn't find the answer since the manual says the way for freezing complete groups. I would like to freeze only a part of my protein and permit the completed optimization of the rest. For example, my protein group has 5 protein chains with 42 residues each of them. I would like to freeze (in all directions) the alfa Carbon atoms for residues 18-42 for each chain. Does somebody know if it is possible to do such thing with GROMACS? Can somebody help me?Thanks a lot, in advanceMarcelo
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