[gmx-users] Problem with Position Restraints (before running SMD)!

[Justin A. Lemkul]

Talal E. AlOtaibi wrote:

> 
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>      1    1       1000       1000       1000
> 1330    1       1000       1000       1000
> 1426    1       1000       1000       1000
> 1437    1       1000       1000       1000
> 1548    1       1000       1000       1000
> 
> #endif

More to the point, this will fail and should have raised a fatal error in 
grompp.  You're putting restraints on atoms that can't possibly exist in water. 
  The numbering is done per [moleculetype] so a position restraint directive for 
water can only have numbers 1, 2, and 3 (OW and the two HW atoms).

If you're trying to restrain atoms in a protein, you have to create a separate 
[position_restraints] directive within the protein's [moleculetype].  See the 
wiki for an example.

-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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