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.
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