[gmx-users] Pull code for Constraint

[xu zhijun]

Hi,

I try to pull the small molecule from the bulk solution to the surface by the Constraint function.
However, it seems that it does not work well.

Here my part of run parameters about the Constraint in my mdp file

##############################

constraints     = all-bonds; hbonds; all-bonds
constraint-algorithm     = Lincs

pull            = constraint
pull_geometry   = distance
pull_dim        = N N Y
pull_ngroups    = 1
pull_group0     = Surface
pull_group1     = Protein
pull_nstxout    = 1000
pull_nstfout    = 1000
pull_rate1      = -0.001
pull_init1      = 1.73331
##########################

Based my understanding, the pull_rate1 is about -0.001/ps.
That means in the pullx.xvg file, the distance shoud be as follows (only the z-distance shown, time step is 1fs.)
1.73331
1.72231
1.72131
1.72031
.
.
However, in my simulation, the results from the simulation is as follow:
1.73331
1.71154
1.75043
1.73213
1.78065
1.79769
1.84298
1.87008

It seems some force has been imposed on the pull molecules.
But in the pullf.xvg the force is ZERO.
I used the latest gromacs version, But for the gromacs4.0 it works very well (works as what I think).
Can someone help me about the issue?

Thanks a lot

Jerry

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