From: sunyeping (sunyeping_at_aliyun.com)
Date: Wed Apr 26 2017 - 12:51:17 CDT
I am trying to do ABF simulation on a protein with a workstation with two c2050 GPU. The colvariable I choose is distance. If the distance is the distance between two atoms (group1 and group2 both contain one atom), the computational speed seems to be normal (about 0.3 day/ns). However, if the distance I define is that between the centers of mass (COM) of two protein subunits (group1 and group2 both contain about 6000 atoms, the computational speed becomes very low (2 day/ns). When I check the GPU ultility, I find the two atom distance simulation has a relatively higher GPU utility (60%), but the two subunit COM distance simulation has a very low GPU utility (4%). How can the atom numbers defined in the distance colvariables affact the GPU utility? Is there any method to improve this GPU utility and computational speed in the COM distance ABF simulation?
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