From: Hyonseok Hwang (danggi_at_northwestern.edu)
Date: Thu Feb 05 2004 - 15:41:49 CST
Hi,
I had the same problem as you, and my temporary solution to that was this :
freeEnergy on
freeEnergyConfig {
urestraint {
dist group {(N,CA,C): (MOL,1),(MOL,2),(MOL,3),(MOL,4)
(MOL,5),(MOL,6),(MOL,7),(MOL,8)}
(SOLV, 795) kf=20, ref=20.0
}
mcti { |
task = stepup |
equiltime = 400 ps |
accumtime = 200 ps | <--- I added this part.
numsteps = 1 |
print = 2.0 ps |
} |
}
Then you can make the restraint you want even if we have one thing we
don't want : the free energy calculation. Anyway, seems like it works,
but it doesn't look nice and I think there should be better solution.
-Hyon
Simon Sharpe wrote:
> Hi,
>
> I have been attempting to apply dihedral and distance restraints to a
> protein within a NAMD simulation. I would like to apply these restraints
> during minimization/equilibrium runs. I have tried variations on the
> following script within the .conf file (increasing the value of kf,
> bound/fixed restraints), but the restraints are not being applied. Can
> anyone tell me what is missing here?
>
> freeEnergy on
>
> freeEnergyConfig {
>
> urestraint {
> dist (U, 13, C) (U, 13, CG) kf=20 ref=3.85
>
> dist (U, 11, C) (U, 13, CD) kf=20 ref=3.4
>
> dist (U, 12, C) (U, 13, CG) kf=20 ref=4.3
>
> dihe (U, 11, C) (U, 12, N) (U, 12, CA) (U, 12, C) barr=20 ref=74
> dihe (U, 12, N) (U, 12, CA) (U, 12, C) (U, 13, N) barr=20 ref=12
>
> dihe (U, 12, C) (U, 13, N) (U, 13, CA) (U, 13, C) barr=20 ref=-96
> dihe (U, 13, N) (U, 13, CA) (U, 13, C) (U, 14, N) barr=20 ref=124
>
> dihe (U, 13, C) (U, 14, N) (U, 14, CA) (U, 14, C) barr=20 ref=-100
> dihe (U, 14, N) (U, 14, CA) (U, 14, C) (U, 15, N) barr=20 ref=119
> }
> }
>
> Thanks,
> Simon
>
> __________________________________
>
> Simon Sharpe
> Laboratory of Chemical Physics, NIDDK
> National Institutes of Health
> 9000 Rockville Pike
> Bethesda, MD 20892
> _________________________________
>
>
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