Dear all,
My system includes some water(2226 water molecules(spc/e)) and a membrane(4000 carbon atoms,no charge) consists of amorphous carbon,so I must calculate electrostatic force.My box is 4*4*17.5(nm^3).Energy minimization is very slow compare with gromacs when I minimize my system.My parameters is in in.pore file.I want to know why Energy minimization is so slow,and whether this problem rises from calculation method of electrostatic force?
PS:I try Ewald,Ewald/n and pppm, but calculation speed has no change.
My output is as below(outstep=1):
Scanning data file ...
2 = max bonds/atom
1 = max angles/atom
Reading data file ...
orthogonal box = (0 0 0) to (40 40 175)
2 by 2 by 2 processor grid
14180 atoms
6452 bonds
3226 angles
Finding 1-2 1-3 1-4 neighbors ...
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
4502 atoms in group membrane
9678 atoms in group water
WARNING: Resetting reneighboring criteria during minimization (min.cpp:160)
PPPM initialization ...
G vector = 0.241058
grid = 27 27 192
stencil order = 5
RMS precision = 6.92134e-06
using double precision FFTs
brick FFT buffer size/proc = 64800 31360 38880
Setting up minimization ...
Memory usage per processor = 385.248 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = 427441938.7536 KinEng = 8600.2259 Temp = 203.4839
PotEng = 427433338.5277 E_bond = 427921864.9191 E_angle = 2832.1927
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -3144.4723
E_coul = -341319.3452 E_long = -146894.7666 Press = 7977553.5435
---------------- Step 1 ----- CPU = 8.9117 (sec) ----------------
TotEng = 294657688.4231 KinEng = 8600.2259 Temp = 203.4839
PotEng = 294649088.1973 E_bond = 301574438.2652 E_angle = 144248.6024
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -3118.5015
E_coul = -6920012.4387 E_long = -146467.7302 Press = 15566841.4530
---------------- Step 2 ----- CPU = 17.8243 (sec) ----------------
TotEng = 285016666.3171 KinEng = 8600.2259 Temp = 203.4839
PotEng = 285008066.0913 E_bond = 291848543.8045 E_angle = 155350.0846
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -3168.2735
E_coul = -6846240.9573 E_long = -146418.5670 Press = 16097328.0820
---------------- Step 3 ----- CPU = 26.7381 (sec) ----------------
TotEng = 273479882.9103 KinEng = 8600.2259 Temp = 203.4839
PotEng = 273471282.6844 E_bond = 280125990.2129 E_angle = 171839.8348
E_dihed = 0.0000 E_impro = 0.0000 E_vdwl = -3258.2561
E_coul = -6676920.6418 E_long = -146368.4653 Press = 16718244.9397
in.pore (1.81 KB)