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

[David van der Spoel]

Arneh Babakhani wrote:
> Can you use this freezegroups function during a minimizaiton?  (say if 
> you wanted to minimize solvent around your protein, while keeping the 
> protein fixed?)
please try before you buy, sorry before asking questions...
this should work anyway.
> 
> 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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>>
>>
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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