fix spring and periodic boundaries

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1

Hi,

I’ve been trying to use fix spring in the couple mode to perform umbrella sampling simulations and found that when separation vector between the two fix groups crosses a periodic boundary the forces/energy from the fix are incorrect (via comparing the forces/energies output from the fix to the analytic spring force/energy).

Checking the code I found that the minimum image convention wasn’t being applied when the separation vector between the groups was calculated.

  • specifically
    dx = xcm2[0] - xcm[0] - xc;
    dy = xcm2[1] - xcm[1] - yc;
    dz = xcm2[2] - xcm[2] - zc;

When I changed this to

dx=xcm2[0]-xcm[0];
dy=xcm2[1]-xcm[1];
dz=xcm2[2]-xcm[2];
domain->minimum_image(dx,dy,dz);
dx-=xc;
dy-=yc;
dz-=zc;

(I confess I have only checked the case when the xc=yc=zc=0 but I think the should be subtracted off after the minimum image correction) the output from the fix agrees with the analytic value. I can’t think of any reason why the minimum image convention wasn’t being applied here (but am prepared to be corrected) - this would also affect simulations where the separation between the groups is comparable to half the box length.

Regards,
David

2

The doc page explains that the COM (of each group in this case)
in computed in coordinates unwrapped by the image flags. When
this is done I don't think it should be necessary (or even correct
in some cases) to further apply minimum image corrections. What
is the geometry of your model, where this doesn't work? Also, I think
there are cases where people want to use fix spring with springs
longer than 1/2 the box. The unwrapping method should work
in any scenario, provided the initial image flags are set appropriately.
Axel may want to comment.

Steve

3

Hi Steve,

Embarrassingly after putting together test input files I found that the
original version was indeed giving the correct answer - guess the problem
must be elsewhere

Regards,
David