[gmx-users] harmonic distance restraints

[Justin A. Lemkul]

francesca vitalini wrote:
> Hi all,
> I'm sorry for the dumb question but I need to put harmonic restraints on 
> my peptide and I cannot find the right command. So, looking on the how 
> tos link in the gromacs website I understand that I need to add to my 
> topology file a posre.itp file with the section [ distance_restraints ] 
> specified with type 6. However I cannot find the command to generate 
> this .itp . On the contrary, for positions restraints there is the genpr 
> command that does it, so I'm looking for the equivalent for the distance 
> restrains. Can anyone help? Btw, I'm using GROMACS 3.3.1,

Unfortunately version 3.3.1 cannot do this automatically for you.  You have to 
write the directive by hand using the manual as guidance.  Newer Gromacs 
versions have options within genrestr (the updated version of genpr) that can 
write distance restraint matrices for selected groups.

Note that the [distance_restraints] directive need not be contained within 
posre.itp; it can be anywhere within the [moleculetype] to which it applies.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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