I performed a minimization simulation of a water box using the tip3p water model in NAMD. The water box was in a sphere of radius 20nm and sphericalBCk1 of 10. The water box changed its shape from a cube to a sphere (almost). My question is why is the water changing its shape when the volume is supposed to be constant?
Martin Klvana
Isn't the sphere imposed by setting the spherical boundary condition with sphericalBCk1 parameter? Why do you define a water box if you want to simulate sphere? Or, why do you define spherical boundary condition if you want to simulate box?
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Meisam Karimi Rad
Hi Ashutosh
See the link below, I hope it helps you
https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2010-2011/0369.html
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