Hello I am trying to perform a CG simulation on the solvated protein but there is one question that I would like to ask for suggestion. The problem is: the volume of the periodic box varied a lot depending on the Van der Waals distance of the CG water molecule.
I guess the volume variation is because of the system needs to relax to the correct density, since the number of water molecule is depending on the Van der Waals distance. Is it reasonable if I start the simulation after the volume become stable under position restraint? Thanks in advance for reading this post. -- Kuang-Yu Chang Institute of Bioinformatic and Structural Biology National Tsin Hua University 101, section 2, Kuang-Fu Road, Hsinchu 30013 Taiwan
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