In my original studio I have a Mac Pro late 2013 trashcan connected to 2 daisy-chained Blackmagic Multidock 2 (thunderbolt 2) units (the older, now discontinued Multidock model). I am in the process of duplicating my rig for a second studio. Provisional tests using a SGI R4400 processor would suggest CPU times increase by a factor of 2.5 to 3.TL/DR - How do I connect two Multidock 10G's to a Mac Pro late 2013 to achieve minimum 20Gbps speed? Specific cable/adapter path appreciated. Run times on the SGI R4400 and R5000 processors are much longer.
The CPU times for several different sized systems are given in Jackson et al. Inputing the control parameters that control these factors are described in the MultiDock user-manual (PDF). The number of sidechain interactions is controled by the extent of the protein-protein interface, the extent of the multiple copy region and the extended fixed boundary region surrounding it. This determines the memory requirements of the program since the fewer the number of residue-residue sidechain interactions the less memory is required. For each cycle of Mean Field Optimisation all residue-residue sidechain interactions (up to 300,000) are pre-calculated and stored by the program. The main MultiDock algorithm uses a multiple copy representation of side chains. The memory requirements for the present version of MultiDock is 61 Mb. They were developed under SGI Irix versions 5.3 and 6.2. The series of programs comprising MultiDock are available only as executables.
1998.Īt present MultiDock is only available for SILICON GRAPHICS WORKSTATIONS or LINUX i386 For a detailed description of the program and application to protein-protein systems see Jackson et al. The results are encouraging for Protein-Inhibitor systems. MultiDock has been tested by performing refinement of large numbers of structures generated by FTDock on several protein-protein systems. MultiDock also implements a rigid-body energy minimization routine which is performed to relax the interface.
VIEVU MULTIDOCK MANUAL FULL
MultiDock implements the self consistent Mean Field Optimisation procedure ( Koehl & Delarue 1994) but using a full conventional molecular mechanics force field with scaling of van der Waals and electrostatic interactions for unrealistically close atomic contacts. The protein is described at the atomic level by electrostatic and van der Waals interactions in which the sidechains are modelled by a multiple copy representation according to a rotamer library on a fixed peptide backbone. The program models the effects of side-chain conformational change and the rigid-body movement of the interacting proteins during refinement. The motivation for this work was to provide a rapid energy refinement protocol for the large number of putative docked complexes produced by rigid-body docking programs such as FTDock or DOCK.
VIEVU MULTIDOCK MANUAL MANUAL
The program MultiDock was developed to provide a method for refining the interface between two proteins at the atomic level given an initial docked complex generated by a docking algorithm or manual docking procedure. MultiDock (v1.0) (Multiple copy side-chain refinement of Protein-Protein interfaces)
Biomolecular Modelling Group at ICRF : 3D-Dock Suite : MultiDock
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