AMBER Archive (2004)

Subject: AMBER: NMR restraint in sander

From: Lishan Yao (yaolisha_at_msu.edu)
Date: Tue Mar 09 2004 - 08:19:30 CST

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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