[gmx-users] dihedral

[Justin A. Lemkul]

Francesco Oteri wrote:
> Dear gromacs users,
> I'm trying to restrain the value of a particular dihedral using the 
> section "[ dihedral_restraints ]" :
> 
> [ dihedral_restraints ]
>  ; ai             aj        ak        al    type    label       phi      
> dphi kfac power
>  13919 13915 13921 13922    1          1      -67.19       0     1    4
> 
> I ran an energy minimization through
> mdrun_d -deffnm 01em -v -debug 6
> 
> but, unfortunately, the values are far from the wanted value ( in 
> radians -67.19 = -1.17)  as grep reveals:
> 
> grep dihres mdrun_d.debug
> dihres[0]: 12650 12647 12651 12652 : phi=-1.090441, dphi=0.000000, 
> kfac=100.000000, power=4, label=1
> dihres[0]: 12650 12647 12651 12652 : phi=-1.090497, dphi=0.000000, 
> kfac=100.000000, power=4, label=1
> dihres[0]: 12650 12647 12651 12652 : phi=-1.090586, dphi=0.000000, 
> kfac=100.000000, power=4, label=1
> dihres[0]: 12650 12647 12651 12652 : phi=-1.090734, dphi=0.000000, 
> kfac=100.000000, power=4, label=1
> dihres[0]: 12650 12647 12651 12652 : phi=-1.090996, dphi=0.000000, 
> kfac=100.000000, power=4, label=1
> dihres[0]: 12650 12647 12651 12652 : phi=-1.091487, dphi=0.000000, 
> kfac=100.000000, power=4, label=1
> dihres[0]: 12650 12647 12651 12652 : phi=-1.092475, dphi=0.000000, 
> kfac=100.000000, power=4, label=1
> dihres[0]: 12650 12647 12651 12652 : phi=-1.094620, dphi=0.000000, 
> kfac=100.000000, power=4, label=1
> dihres[0]: 12650 12647 12651 12652 : phi=-1.099689, dphi=0.000000, 
> kfac=100.000000, power=4, label=1
> dihres[0]: 12650 12647 12651 12652 : phi=-1.112823, dphi=0.000000, 
> kfac=100.000000, power=4, label=1
> dihres[0]: 12650 12647 12651 12652 : phi=-1.147934, dphi=0.000000, 
> kfac=100.000000, power=4, label=1
> dihres[0]: 12650 12647 12651 12652 : phi=-1.230998, dphi=0.000000, 
> kfac=100.000000, power=4, label=1
> dihres[0]: 12650 12647 12651 12652 : phi=-0.342237, dphi=0.000000, 
> kfac=100.000000, power=4, label=1
> dihres[0]: 12650 12647 12651 12652 : phi=-1.931253, dphi=0.000000, 
> kfac=100.000000, power=4, label=1
> dihres[0]: 12650 12647 12651 12652 : phi=1.093490, dphi=0.000000, 
> kfac=100.000000, power=4, label=1
> dihres[0]: 12650 12647 12651 12652 : phi=-0.846042, dphi=0.000000, 
> kfac=100.000000, power=4, label=1
> dihres[0]: 12650 12647 12651 12652 : phi=1.893053, dphi=0.000000, 
> kfac=100.000000, power=4, label=1
> dihres[0]: 12649 12646 12650 12651 : phi=-0.523006, dphi=0.000000, 
> kfac=100.000000, power=4, label=1
> dihres[0]: 12649 12646 12650 12651 : phi=2.245932, dphi=0.000000, 
> kfac=100.000000, power=4, label=1
> dihres[0]: 12649 12646 12650 12651 : phi=-1.518727, dphi=0.000000, 
> kfac=100.000000, power=4, label=1
> dihres[0]: 12649 12646 12650 12651 : phi=1.665189, dphi=0.000000, 
> kfac=100.000000, power=4, label=1
> dihres[0]: 12648 12645 12649 12650 : phi=-1.820232, dphi=0.000000, 
> kfac=100.000000, power=4, label=1
> dihres[0]: 12648 12645 12649 12650 : phi=1.414995, dphi=0.000000, 
> kfac=100.000000, power=4, label=1
> dihres[0]: 12648 12645 12649 12650 : phi=-2.154156, dphi=0.000000, 
> kfac=100.000000, power=4, label=1
> 
> Do I made any error or did I miss something?
> 

A restraint is only a biasing potential; the value with not remain fixed and for 
the most part you are only a few percent off.  Some of the values deviate pretty 
substantially - what is the average of the dihedral?

One option is to increase kfac to make the restraint stronger and further bias 
the dihedral towards the target value.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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