[gmx-users] Help!! Large VCM(group rest):

Linda fuwei at adrik.bchs.uh.edu
Tue Mar 2 21:40:02 CET 2004

Dear gromacs user,

     I did MD simulation in rectungular water box on four systems, the start structure comes from crystal structure and verified by insightII. Then I did minimizaiton by sd and cg with gromacs3.2 version on itanium clusters. Then heat the protein, after 500ps equalibration, and begin to do long time MD simulation. The special thing is that the protein has a big long loop, every time I do MD (use shake constraint altorithm and 2fs timestep), the simulation is always crashes and complains the large VCM error. For example, a simulation on one system is crashes after 1.5 ns. The log file is as following:
           Step           Time         Lambda
         781000     1562.00012        0.00000

   Energies (kJ/mol)
           Bond          Angle    Proper Dih.  Improper Dih.          LJ-14
    5.20232e+03    7.31688e+03    2.74605e+03    2.34688e+03    3.41803e+03
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coulomb (LR)      Potential
    4.48288e+04    2.67089e+05   -1.78180e+06   -3.06613e+05   -1.75547e+06
    Kinetic En.   Total Energy    Temperature Pressure (bar)
    3.14063e+05   -1.44140e+06    2.99503e+02    1.07471e+02

t = 1562.008 ps: Water molecule starting at atom 9027 can not be settled.
Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinates
Large VCM(group rest): 1240285.25000, 1556922.00000, 17160415232.00000, ekin-cm:  1.06480e+26

I checked the structure at 1562ps, the 9027 atom is the oxygen of water, which is far from protein and box bother. So, I do not know why it complains such error? The energy and tempature are OK. I constrain the translation of protein by "comm_grps =  Protein", but I do found the protein rotates, but no atoms is out of water box. 

The other thing is that the system is pretty big, the total atom number is above 120,000, does it has something to do with the crashing? 

I have searched the GROMACS mailing list archive and found that somebody also encouter such problem, but the answer is just to verify the bad contacts. But it did not help me because I have optimized the system well (use cg with gmx2.0 version), and it complains a oxygen atom from a water, it is far from both the protein and box bother. If it has bad contacts, it should be crashes at first several hundred ps MD simulation, so it seems to be wired. Anyone can help??? I really need help!! Any help will be highly appreciated!

By the way, the .mdp file is:

title               =  my protein
cpp                 =  /lib/cpp
constraints         =  hbonds
constraint-algorithm = shake
integrator          =  md
dt                  =  0.002    ; ps !
nsteps              =  25000000    ; total 50ns.
nstcomm             =  1
comm_grps           =  Protein
nstxout             =  1000
nstvout             =  1000
nstfout             =  0
nstxtcout           =  1000
nstlog              =  1000
nstenergy           =  1000
nstlist             =  10
ns_type             =  grid
coulombtype         =  PME
rlist               =  0.9
rcoulomb            =  0.9
rvdw                =  0.9
fourierspacing      =  0.12
pme_order           =  4
optimize_fft        =  yes
; Berendsen temperature coupling is on in two groups
Tcoupl              =  berendsen
tc-grps             =  Protein  SOL   NA   CL
tau_t               =  0.1      0.1   0.1  0.1
ref_t               =  300      300   300   300
energygrps          =  Protein SOL NA CL
; Pressure coupling is on
Pcoupl              =  berendsen
tau_p               =  1
compressibility     =  4.5e-5
ref_p               =  1.0
; Generate velocites is on at 300 K.
gen_vel             =  no
gen_temp            =  300.0
gen_seed            =  173529

I checked several times and do not found any problem. 

Cheers, Linda

  Wei Fu (Linda)
  Postdoctoral Research Associate
  Department of Biology and Biochemistry 
  University of Houston
  4800 Calhoun Rd. HSC #402C
  Houston, TX 77204-5001   USA
  Phone:713-743-8355(o)  713-795-9270(h) 
  Email: fuwei at adrik.bchs.uh.edu

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