青 叶 wrote:
I did a energy minimization on a system contain one [AuCl4]- and 503
water moleculars, by using a self-define non-bond interaction (which is
obtain from ab-initio calculation), my em.mdp file is as follow:
title = yqq
cpp = /usr/bin/cpp ; the c pre-processor
define = -DFLEXILBE
constraints = none
integrator = steep
energygrps = AU CL OW H
energygrp_table = AU OW AU H CL OW CL H
dt =0.002; ps!
nsteps =40000
nstlist =10
ns_type =grid
rlist =0.9
coulombtype =User
rcoulomb =0.9
vdwtype =User
rvdw =1.0
fourierspacing =0.12
fourier_nx =0
fourier_ny =0
fourier_nz =0
pme_order =4
ewald_rtol =1e-5
optimize_fft =yes
;
; Energy minimizing stuff
;
emtol =500.0
emstep =0.005
and meanwhile, I have modifide the ffG43a1.rtp, ffG43a1bon.itp,
ffG43a1nb.itp files in order to include the relative parameters. Then
add a table.xvg (actually the default 6-12 Lennard Jones potential form,
I just renamed it so it will be read for describing the interaction of
atom pairs which are not list in the energygrp_table section) and four
table****.xvg contain the interaction information of AU OW, AU CL, CL
OW, CL H.
but unfortunatly, the corresponding em.log file is follow:
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 500
Double precision normally gives you higher accuracy.
You might need to increase your constraint accuracy, or turn
off constraints alltogether (set constraints = none in mdp file)
Steepest Descents converged to machine precision in 12 steps,
but did not reach the requested Fmax < 500.
Potential Energy = -3.5686449e+04
Maximum force = 1.3609032e+04 on atom 1236
Norm of force = 1.6019813e+03
M E G A - F L O P S A C C O U N T I N G
RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy
T=Tabulated W3=SPC/TIP3p W4=TIP4p (single or pairs)
NF=No Forces
Computing: M-Number M-Flops % Flops
-----------------------------------------------------------------------
VdW(T) 1.011752 54.635 16.6
Coul(T) + VdW(T) 2.659114 180.820 55.0
Outer nonbonded loop 0.261041 2.610 0.8
NS-Pairs 4.096803 86.033 26.2
Reset In Box 0.012096 0.036 0.0
Shift-X 0.018168 0.109 0.0
CG-CoM 0.018168 0.055 0.0
Bonds 0.000048 0.003 0.0
Angles 0.000072 0.012 0.0
Impropers 0.000024 0.005 0.0
Virial 0.018708 0.337 0.1
Settle 0.012072 3.899 1.2
-----------------------------------------------------------------------
Total 328.553 100.0
-----------------------------------------------------------------------
R E A L C Y C L E A N D T I M E A C C O U N T I N G
Computing: Nodes Number G-Cycles Seconds %
-----------------------------------------------------------------------
Neighbor search 1 12 0.844 0.8 77.7
Force 1 12 0.180 0.2 16.5
Constraints 1 23 0.004 0.0 0.4
Rest 1 0.059 0.1 5.4
-----------------------------------------------------------------------
Total 1 1.086 1.0 100.0
-----------------------------------------------------------------------
NODE (s) Real (s) (%)
Time: 1.000 1.000 100.0
(Mnbf/s) (MFlops) (steps/hour)
Performance: 3.671 328.553 43200.0
Finished mdrun on node 0 Wed Oct 21 23:38:48 2009
the force is very large and I have tried to adjust "emstep" and other
options but seems has no influence on the result, can anyone help me on
this problem, any suggestion will be very, very grateful. Thank you.
By the way, I have ajusted the No. of water moleculars in the simulation
box but almost has no infulence on the result.
The magnitude of the PE is such that you've probably not made any
catastrophic errors. Make sure you get the sign of the table columns
correct for various derivatives correct. Otherwise, have a look at atom
1236 and see what might be wrong in that region.
Mark
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