Calcium (other ions) with gromacs-openmm

The functionality of OpenMM will (eventually) include everything that one would need to run modern molecular simulation.
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Jiri Cerny
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Calcium (other ions) with gromacs-openmm

Post by Jiri Cerny » Wed May 19, 2010 7:58 am

Hi, I wonder what would be the scaling factor I have to add to the getObcScaleFactors() to allow calcium ions simulations. In fact, would it be the only modification necessary, or are there any other reasons why only so few elements are defined there?

thanks, JC
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Mark Friedrichs
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RE: Calcium (other ions) with gromacs-openmm

Post by Mark Friedrichs » Wed May 19, 2010 11:17 am

The OBC parameter values were obtained from Jay Ponder's Tinker http://dasher.wustl.edu/tinker. I am not sure why more ions were not included there. I am unaware of any other modifications to the program/algorithm that would be needed to include Ca or other ions w/ missing parameters. The Tinker default value for the scaling factor is 0.8
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Jiri Cerny
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RE: Calcium (other ions) with gromacs-openmm

Post by Jiri Cerny » Thu May 20, 2010 2:06 am

Thanks for the answer, in the tinker sources (ksolv.f) I have found extra params for F and Fe (with the H C N O P S already present in the md_openmm.cpp). It seems that the getObcScaleFactors() is crippled by the exit call only (even when the already assigned default 0.8 factor could be used). Well, I will remove that exit call and pretend that 0.8 is good enough ;-)
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