Hi,
What you need is perhaps weight change, you can find it in section 2 of
amber manual.
Cheer,
Guanglei
Lishan Yao wrote:
> Hi:
> I want to rotate a dihedral angle from 0 to -70 in 100000 steps MD
> simulation (5000 steps for each rotation). Here is the restraint file:
>
> &rst iat = 918, 921, 924, 926, nstep2=100000,ialtd=0,
> ifvari=1,ninc=5000,
> r1 = -50, r2 = -0.0, r3 = -0.0, r4 = 50,
> rk2 = 100.0, rk3 = 100.0,
> r1a = -120, r2a = -70.0, r3a = -70.0, r4a = -20,
> rk2a = 100.0, rk3a = 100.0,
> &end
> My question is how sander sets the target dihedral angle during the
> change? Seems to me it could be either 0+j*(-70-0)/20(j=0,1,...19), or
> 0+j*(-70-0)/(20-1)(j=0,1,....19). My simulation shows the first one
> might be what sander does. But the second one makes more sense to me.
> But I don't know which one sander uses.
>
> Best,
> Lishan
>
>
>
>
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Received on Tue Mar 09 2004 - 15:53:01 PST
