[gmx-users] freeze the particular residues in NPT-NVT

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Dear gmx,


I have used freezgreps for 20 residues of 152 residues contained protein and the it took well for energy minimization steps according to the input given on mdp and index files. However, when i go for further NPT steps it gives following error.


Fatal error:
Group Protein referenced in the .mdp file was not found in the index file.
Group names must match either [moleculetype] names or custom index group
names, in which case you must supply an index file to the '-n' option
of grompp.


I have rechecked the reference structure (em.gro) with index and nvt.mdp files but all of their index numbers are correct. can anyone tell me how would avoid them? Thanks in advance.



On Mar 19, 2013, at 11:45 AM, Justin Lemkul wrote: 

> On 3/19/13 5:44 AM, ��������������� wrote: 
>> Anyone tell me how do I freeze the particular residues in NPT-NVT 
>> equillibrium steps ? I want them in same conformation as pdb for 
>> further production run ? Thanks in advance 
>> 
> 
> Use freezegrps or strong position restraints. 

But note that if you release frozen groups after equilibration your 
system may need further time to equilibrate. 

Erik