[gmx-users] Dihedral restraints

[santhosh]

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





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