[gmx-users] Restarting AFM pulling

Semen Esilevsky yesint4 at yahoo.com
Wed May 23 11:29:36 CEST 2007

Hello everyone,
I'me trying to run a very long simulation with the AFM pulling, which should be partitioned into many smaller pieces. However, this seems that the pull code does not preserve the force even if the position of the spring is set to what was observed at the end of the previous run.
Here is an example. I have one pull group pulled in Z direction, so in the .pdo file, according to the manual, I have the time, the position of the reference, the position of the pull group and the pos. of the spring.
The end of the .pdo from the first run looks like this:

12.000001       4.537002        1.228887        1.279260

I start new run with the afm_init1 = 0 0 -3.257742   (the last number is 1.279260-4.537002 i.e. relative pos. of the spring as it should be).
And in the beginning of the new run I get:

12.000001       4.537002        1.228887        1.291260

So, why the spring goes to 1.291260 if I said it to be at 1.279260 ?!  This prodices a sudden jump at the restart point and I have no idea how large this jump can be in real simulation.
Is this a bug or I misunderstand something?


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