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fhh2626 / BFEE2

binding free energy estimator 2
GNU General Public License v3.0
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Problem with box size #99

Open groponp opened 1 year ago

groponp commented 1 year ago

Dear,

I am experiencing an error, which I think is simple to fix. What happens is that when you balance your system independently, and use the reset files to prepare the data for the free energy calculation, the program over-estimates the values ​​of the center and size vectors of the box, this it results in "the box is too small" errors, I think they could add an option to be able to pass the xsc file to it so that it can read it directly from there. I have experienced this several times, although with a manual correction everything runs fine, but since there are many files where it has to be corrected, it becomes tedious.

fhh2626 commented 1 year ago

Hi, groponp,

I understand you problem. You can always set WrapAll on in your NAMD config file to circumvent this issue.

I will think if it is possible to read an xsc file. The difficulty is that BFEE2 will extend the water box in step 7, but this step is somewhat tricky if the structure of the box is not correct.

Good luck, Haohao

groponp commented 1 year ago

Ok, Prof. I will can try it in future simulation and check if it do not given any error. Thanks.