Gromacs CPU的问题
跑了能量最小化以后显示这个，我的GPU卡很差，GTX750TI，出现这种负载颠倒的情况能够优化吗？NOTE: The GPU has >20% more load than the CPU. This imbalance causes
performance loss, consider using a shorter cut-off and a finer PME grid.
NOTE: 14 % of the run time was spent in pair search,
you might want to increase nstlist (this has no effect on accuracy)
gromacs要注意cpu和gpu的搭配，gromacs设置了gpu用于计算非键相互作用，cpu计算成键相互作用。所以如果cpu快了，gpu慢了，那么cpu就要等gpu，反之则gpu等cpu，这样就导致了计算速度下降。 川大-灰太狼 发表于 2015-10-25 23:22
gromacs要注意cpu和gpu的搭配，gromacs设置了gpu用于计算非键相互作用，cpu计算成键相互作用。所以如果cpu ...
嗯嗯，好的，谢谢灰太狼o(∩_∩)o 川大-灰太狼 发表于 2015-10-25 23:22
gromacs要注意cpu和gpu的搭配，gromacs设置了gpu用于计算非键相互作用，cpu计算成键相互作用。所以如果cpu ...
灰太狼大大，可以理解成只要gpu速度快于cpu就不会拖计算后腿吗？ atmdd 发表于 2015-10-30 11:49
灰太狼大大，可以理解成只要gpu速度快于cpu就不会拖计算后腿吗？
两个要搭配好，谁都不能慢，就如同水桶理论一样：） 川大-灰太狼 发表于 2015-10-30 14:01
两个要搭配好，谁都不能慢，就如同水桶理论一样：）
那这个主要是要修改md.mdp中的哪个呢？
title = Protein-ligand complex MD simulation
; Run parameters
integrator= md ; leap-frog integrator
nsteps = 15000000 ; 2 * 15000000 = 30000 ps (30 ns)
dt = 0.002 ; 2 fs
; Output control
nstxout = 0 ; suppress .trr output
nstvout = 0 ; suppress .trr output
nstenergy = 5000 ; save energies every 10.0 ps
nstlog = 5000 ; update log file every 10.0 ps
nstxout-compressed= 5000 ; write .xtc trajectory every 10.0 ps
compressed-x-grps = System
energygrps = Protein EVO
; Bond parameters
continuation = yes ; first dynamics run
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
cutoff-scheme = Verlet
ns_type = grid ; search neighboring grid cells
nstlist = 10 ; 20 fs, largely irrelevant with Verlet
rcoulomb = 1.4 ; short-range electrostatic cutoff (in nm)
rvdw = 1.4 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing= 0.16 ; grid spacing for FFT
; Temperature coupling
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein_EVO Water_and_ions ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each group, in K
; Pressure coupling
pcoupl = Parrinello-Rahman ; pressure coupling is on for NPT
pcoupltype= isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; assign velocities from Maxwell distribution
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