[gmx-users] distance restrainrts problem

[Mark Abraham]

On 25/04/2010 1:23 AM, Павел Кудрявцев wrote:
> Hi,
> I'm trying to apply some distance restraints to several H-bonds in my
> systems (all in protein) . Due to manual I added following lines
> [ distance_restraints ]
> ; ai     aj     type index type’ low up1  up2 fac
>    3880   4829    1    0     1     0.0 0.22 0.4 1.0
>    3880   7692    1    0     1     0.0 0.22 0.4 1.0
>    4820   6654    1    1     1     0.0 0.22 0.4 1.0
>    4820   6700    1    1     1     0.0 0.22 0.4 1.0
>    6652   6889    1    2     1     0.0 0.22 0.4 1.0
>    6652   6856    1    2     1     0.0 0.22 0.4 1.0
> in itp. file

Unless you're trying to do distance restraint averaging "over multiple 
pairs", you don't want to repeat any index values. See manual 4.3.4. I 
don't know if this is the cause of your problem, however.

> and following lines
> disre                    = simple
> disre_weighting          = equal
> disre_mixed              = no
> disre_fc                 = 1000
> disre_tau                = 0
>
> in .mdp file. Next md simulation run fine and after it I see Dist.-Rest.
> option when executing g_energy, but I don't see any distinct influence
> on trajectory - all restrainted distances seems to be free and sometimes
> even exceeding 4 angstrom. I tried to change index, type', disre_fc
> values from 1000 to 200000, but nothing helped.
> Besides that when I'm trying to use g_disre I'm getting following error
> - 'Segmentation fault'

That's not a helpful diagnostic. You're not giving us any information to 
work with... What was your input? What was the output *before* the segfault?

Mark

> So what's wrong and how can I be sure that distance restraints works?
> thanks in advance.
>