[gmx-users] constraint and restraints

[niyaz.sabir]

Dear Tsjerk,
 
Thank you very much. You are always ready to help. 

I have understood and taken your note : "Whether it makes sense is another question. The dynamics is usually coupled throughout the protein." 

With very best regards,
 
Niyaz

  ----- Original Message ----- 
  From: Tsjerk Wassenaar 
  To: Discussion list for GROMACS users ; niyaz.sabir 
  Sent: Monday, October 06, 2014 1:13 AM
  Subject: Re: [gmx-users] constraint and restraints


  Hi Niyaz,


  You can set position restraints for all atoms not in that residue range. Whether it makes sense is another question. The dynamics is usually coupled throughout the protein.


  Cheers,


  Tsjerk


  On Sun, Oct 5, 2014 at 10:03 PM, niyaz.sabir <niyaz.sabir at gmail.com> wrote:

    Dear GROMACS  users,
    Is it possible with Gromacs and how could be done a simulation keeping almost all  protein residues fixed except for instance resi 361-372 ? Will the extraction of resulting rmsd for each residue give some knowledge regarding its flexibility (mobility) ?
    Regards, N.S.
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  Tsjerk A. Wassenaar, Ph.D.