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

[Justin A. Lemkul]

程迪 wrote:
> 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

Coupling the entire system to the same thermostat is likely a poor choice.

> tau_t               =  0.1
> ref_t               =  300

300 K is below the phase transition for DPPC (315 K); do you want a gel-phase 
bilayer?

> ; 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.
> 

You have an extremely large charge group, which could be problematic.  See the 
manual and the numerous threads in the list archive related to this topic.

> 
> 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
> 

It looks simply like your system is blowing up.  Have you done any form of 
energy minimization prior to this MD?

-Justin

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

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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