[gmx-users] Inner product between old and new vector <= 0.0!

[程迪]

Hi, everyone

I used a double precision version of gromacs, to simulate a SiO2 on a DPPC
bilayer.
And here is my md.mdp. I have not add pull code into it.

title               =  fws
cpp                 =  /usr/bin/cpp
constraints         =  all-bonds
constraint_algorithm=  SHAKE
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  50000    ; total 100 ps.
nstcomm             =  1
nstxout             =  500
nstvout             =  0
nstfout             =  0
nstlist             =  10
ns_type             =  grid
rlist               =  1.0
coulombtype         =  PME
rcoulomb            =  1.0
vdwtype             =  cut-off
rvdw                =  1.4
fourierspacing          =  0.12
fourier_nx              =  0
fourier_ny              =  0
fourier_nz              =  0
pme_order               =  6
ewald_rtol              =  1e-5
optimize_fft            =  yes
; Berendsen temperature coupling is on in three groups
Tcoupl              =  berendsen
tc_grps                 = System
tau_t               =  0.1
ref_t               =  300
; Pressure coupling is on
Pcoupl              =  parrinello-rahman
pcoupltype          =  isotropic
tau_p               =  1.0
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  yes
gen_temp            =  300.0
gen_seed            =  173529

and command line

gromppd -f md.mdp -c dppc128_pull.gro -p em.top -o dppc128_pull.tpr -maxwarn
1 -n pull.ndx

NOTE 1 [file md.mdp, line unknown]:
  The Berendsen thermostat does not generate the correct kinetic energy
  distribution. You might want to consider using the V-rescale thermostat.

NOTE 2 [file em.top, line unknown]:
  The largest charge group contains 25 atoms.
  Since atoms only see each other when the centers of geometry of the charge
  groups they belong to are within the cut-off distance, too large charge
  groups can lead to serious cut-off artifacts.
  For efficiency and accuracy, charge group should consist of a few atoms.
  For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.


mdrund -s dppc128_pull.tpr  -v

and here is the output
...
step 100, will finish Mon Mar 29 00:25:14 2010
step 200, will finish Mon Mar 29 00:26:05 2010
step 300, will finish Mon Mar 29 00:23:37 2010
step 400, will finish Mon Mar 29 00:22:22 2010
Inner product between old and new vector <= 0.0!
constraint #96 atoms 17442 and 17453
Wrote pdb files with previous and current coordinates
Inner product between old and new vector <= 0.0!
constraint #14 atoms 17375 and 17392
Wrote pdb files with previous and current coordinates
Inner product between old and new vector <= 0.0!
constraint #13 atoms 17374 and 17392

t = 0.930 ps: Water molecule starting at atom 24890 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates
Segmentation fault



Di Cheng

University of Science and Technology of China
Hefei, Anhui Province 230026
P. R. China
E-mail: chengdi at mail.ustc.edu.cn
Tel.: +86-15321055911
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