[gmx-users] Questions in using non-equilibrium dynamics

[qwp]

Hi David:

I am sure there is no constraints. David van der Spoel

In the mdp file:
; OPTIONS FOR BONDS    
constraints              = none
; Type of constraint algorithm
constraint-algorithm     = Lincs
; Do not constrain the start configuration
unconstrained-start      = yes

and i use the pull code to simulate the same process. 

runtype                  = afm
group_1                  = a_1
reference_group          = a_2
afm_rate1                = 0.0001
afm_dir1                 = 0.0 0.0 1.0
afm_k1                   = 10000
afm_init1                = 0.0 0.0 0.142

The initial gro:

1CNT     C1    1   1.500   1.500   1.571 -0.0488  0.2871  0.0382
1CNT     C2    2   1.500   1.500   1.429  0.2162  0.1612  0.0378

The result gro:

1CNT     C1    1   1.500   1.501   2.561  0.0000  0.0000  0.0001
1CNT     C2    2   1.500   1.500   1.429  0.0000  0.0000 -0.0001

Then I calculate the pull force F(add)= k1*(rate*T-Rij) =10000 *(0.0001*10000-(2.561-1.571))=100pN. Is it right?
The bond force F(bon)=kb*(Rij)=100*(2.561-1.571)=99pN
But at this moment the a_1 atom is still moving!! 

why?

Thank you .

Qi Wenpeng
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