[gmx-users] problem in distance restraint

[Justin Lemkul]

On 1/28/13 2:10 PM, Masomeh Dehghani wrote:
> Dear users
>
>   I have 6 water molecules ,I want to constraint the distance between 6 oxygen  atoms in 0.42 nm  from together.I read GROMACS manual but I had fatal erorr.
>
> Here there is  disres.itp file:
>
> ; Include Distance restraints file
> #ifdef DDISRES
> #endif
> [ distance_restraints ]
> ;ai     aj      type    index   type'   low     up1     up2     fac
>   1      4         1       1       1      0.42    0.42    0.42    2.0
>   1      7         1       2       1      0.42    0.42    0.42    2.0
>   1      10        1       3       1      0.42    0.42    0.42    2.0
>   1      13        1       4       1      0.42    0.42    0.42    2.0
>   1      16        1       5       1      0.42    0.42    0.42    2.0
>

I doubt this approach will work.  Note the functional form provided in the 
manual - if your molecules deviate, I doubt that mdrun will know how to actually 
calculate the energy associated with the deviation.  You need to supply a range 
of values within which the distances may oscillate.

> my topology file:
> ; Include Distance restraint file
> #ifdef DISRES
> #include "disres.itp"
> #endif
>
> my  em.mdp
> define         = -DDISRES
> disres         = simple
>
> error
> WARNING 1 [file em.mdp, line 19]:
>    Unknown left-hand 'disres' in parameter file
>

The keyword is "disre," not "disres."

http://manual.gromacs.org/online/mdp_opt.html#nmr

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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