Hi,<br>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<br>[ distance_restraints ]<br>; ai aj type index type’ low up1 up2 fac<br>
3880 4829 1 0 1 0.0 0.22 0.4 1.0<br> 3880 7692 1 0 1 0.0 0.22 0.4 1.0<br> 4820 6654 1 1 1 0.0 0.22 0.4 1.0<br> 4820 6700 1 1 1 0.0 0.22 0.4 1.0<br> 6652 6889 1 2 1 0.0 0.22 0.4 1.0<br>
6652 6856 1 2 1 0.0 0.22 0.4 1.0<br>in itp. file<br><br>and following lines <br>disre = simple<br>disre_weighting = equal<br>disre_mixed = no<br>disre_fc = 1000<br>
disre_tau = 0<br><br>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.<br>
Besides that when I'm trying to use g_disre I'm getting following error - 'Segmentation fault'<br>So what's wrong and how can I be sure that distance restraints works?<br>thanks in advance.<br><br>