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

[Tsjerk Wassenaar]

Hi Wei,

Though it shouldn't matter, try setting comm_grps to System

Greetings,

Tsjerk

Linda wrote:

>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) 
>  Fax:713-743-8351 
>  Email: fuwei at adrik.bchs.uh.edu
>  http://adrik.bchs.uh.edu/~fuwei/
>**************************************************************
>
>
>
>
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