[gmx-users] Freezing part of the molecules!!!

[Arneh Babakhani]

Can you use this freezegroups function during a minimizaiton?  (say if 
you wanted to minimize solvent around your protein, while keeping the 
protein fixed?)

David van der Spoel wrote:
> Soren Enemark wrote:
>>  Hi Marcelo,
>>  what you need to do is:
>>
>>  1. create an index file (.ndx) with the groups that you want to freeze.
>>     Such an index file should look like:
>>     [ Group1 ]
>>     45 46 47 48 49 ...
>>     [ Group2 ]
>>     106 107 ...
>>     [ Group3 ]
>>     ....
>>
>>     where atoms number 45, 46, 47, 48, and 49 etc belong to your 1st 
>> group and     so on. Remember to use the numbering as it is in the 
>> gro file.
>>     This you can do with "make_ndx -f your_gro_file.gro"
>>
>>  2. Add the folling to your mdp file:
>>     freezegrps = Group1 Group2 Group3 Group4 Group5
>>     freezedim  = Y Y Y  Y Y Y  Y Y Y  Y Y Y  Y Y Y
>>
>>     Note that for each group defined as freezegroup you need to 
>> specify the
>>     dimensions that you want to freeze (x y z). This is done with either
>>     Y or N. So if you want only to freeze Group1 in the z-direction 
>> you write:
>>     freezegrps = Group1
>>     freezedim  = N N Y
>>
>>  All the best,
>>  Soren
>>
>
> Just as a warning: please note that combining:
> constraints + freeze groups + pressure coupling
> will give undefined results.
>
>
>
>> Quoting Marcelo Fabricio Masman <mmasman at gmail.com>:
>>
>>
>>> 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 advance
>>>
>>> Marcelo
>>>
>>
>>
>>
>>
>>
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>
>