Hello All, While doing NMR refinement or custom force addition, it can happen than the force on the system can push the peptide plane atoms out of the plane. [ like the amide bond is pushed out of the plane to satisfy the external force or the omega angle is deformed beyond acceptable values]. To control this behavior, I want to employ dihedral restrains on my system.
I have understood the format and the required steps but the results of a short simulation are not as expected. For example : #18 : C of resid 1 ; 20 : N of resid 2 ; 5 : CA of resid 1 ; 22 : CA of resid 2 # 19 : O of resid 1 ; 21 : H of resid 2. #; ai aj ak al type label phi dphi kfac power 5 18 20 22 1 0 180.000000 4 1 1 19 18 20 22 1 0 0.000000 4 1 1 5 18 20 21 1 0 180.000000 4 1 1 19 18 20 21 1 0 0.000000 4 1 1 In the .mdp file, i have ;dihedral restraints dihre = yes dihre_fc = 50 ; or whatever value you desire nstdihreout = 50 I ran a short 2000 step simulation and over the period of time I tracked the four dihedral values, every row is a timestep. #the first line is the restrained reference value. 180 0 180 0 -147.287215895064 9.45865329024718 -159.203988508429 -2.45811932311724 -111.050389450397 -81.9953887566147 -92.0822326476887 -63.0272319539059 -110.958596230868 -73.8376501933164 -92.9130172813275 -55.7920712437757 -112.517830994369 -59.5426717504823 -102.604122568900 -49.6289633250131 -100.996135584400 -74.4228693635875 -87.2297061267471 -60.6564399059348 -93.9669086707340 -57.7658765173159 -86.3382092652599 -50.1371771118417 -95.0591618723864 -66.9832558152160 -85.0934054990846 -57.0174994419143 -94.2190629339560 -52.6947808390542 -91.1562898592925 -49.6320077643907 -87.5354914279667 -69.2330638322494 -73.2840411103266 -54.9816135146093 -112.405078265351 -73.0596345313864 -97.4992184521689 -58.1537747182041 As you can see, the value moves away from the reference value as the simulation goes on. Any hints about any possible mistake in my implementation would be appreciated. Thanks Santhosh -- View this message in context: http://gromacs.5086.n6.nabble.com/Dihedral-restraints-tp5006617.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
