Dear, I am simulating a small protein (less then 50 amino acids) at room temperature, with no additional atoms and/or molecules and/or ions. The simulations seems to proceed ok (in terms of avg. kinetic energy and other energy terms). Then, I take the same protein, and introduce a "surface" to the system. My surface is just a set of identical hard sphere atoms, here is how a surface atom is defined inside my .TOP file: [ atomtypes ] ;name mass charge ptype c6 c12 X 1.000 0.000 X 0.000 0.600E-09 And there are 10 times more surface atoms then protein atoms.
In my .MDP file, there are two energy groups: protein & non-protein. The surface is frozen in all xyz directions. Now, the problem is that with the surface, my protein quickly explodes, and I have no idea why. The surface and protein each coupled to its own thermostat. Your help and ideas/comments are appreciated. Omer. Koby Levy research group, Weizmann Institute of Science. http://www.weizmann.ac.il/sb/faculty_pages/Levy/
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