[gmx-users] problem in distance restraint

[Justin Lemkul]

Please keep the discussion on the gmx-users mailing list.

On 1/29/13 12:20 PM, Masomeh Dehghani wrote:
> Dear Justin
> Have a nice time.
> Thank you for your reply.
> I did  my simulation with distance restraint again.(my system has 6
> water molecule, I want to imose distance restarint between oxygen atoms with
> 0.42 nm together. 1,4,7,10,13,16 are oxygen atoms in system)
> disre.itp:
>
> [ distance_restraints ]
> ;ai     aj      type    index   type   low     up1     up2     fac
>   1      4         1       1       6      0.42    0.43    0.44  1.0
>   1      7         1       1       6      0.42    0.43    0.44    1.0
>   1      10        1       1       6      0.42    0.43    0.44    1.0
>   1      13        1       1       6      0.42    0.43    0.44    1.0
>   1      16        1       1       6      0.42    0.43    0.44    1.0
>   4      7         1       1       6      0.42    0.43    0.44    1.0
>   4      10        1       1       6      0.42    0.43    0.44    1.0
>   4      13        1       1       6      0.42    0.43    0.44    1.0
>   4  16        1       1       6      0.42    0.43    0.44    1.0
>   7      10        1 1       6      0.42    0.43    0.44    1.0
>   7      13        1       1       6      0.42  0.43    0.44    1.0
>   7      16        1       1       6      0.42    0.43    0.44    1.0
>   10     13        1       1       6      0.42    0.43    0.44    1.0
>   10     16        1       1       6      0.42    0.43    0.44    1.0
>   13     16        1       1       6      0.42    0.43    0.44    1.0
>
>   my topology file:
> ; Include Distance restraint file
> #ifdef DISRE
> #include "disre.itp"
> #endif
>
>   em.mdp file:
>
> define          =  -DDISRE
> ; DISTANCE RESTRAINTS
> disre               =  simple
> disre_weighting     =  equal
> disre_fc            =  20
> disre_mixed         =  yes
> disre_tau           =  10
> nstdisreout         =  100
>
>
> and also add these lines :
>
> ; Distance restraints
> define          =  -DDISRE
> ; DISTANCE RESTRAINTS
> disre               =  simple
> disre_weighting     =  equal
> disre_fc            =  20
> disre_mixed         =  yes
> disre_tau           =  10
> nstdisreout         =  100
>
> to pr.mdp and md.mdp files.
> I didn't have any erorr,
>
> but after 500 ps , I checked output and saw 6 water molecules  were
> far from together.
>
> I don't know what I have to do.

Do you have your topology correctly set up such that the water molecules to 
which you are applying restraints are unified in a single [moleculetype]?

-Justin


-- 
========================================

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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