[gmx-users] VCM

[David]

On Mon, 2005-04-04 at 18:57 +0200, Michal Kolinski wrote:
> Hi all
> 
> I’m simulating membrane made of three types of lipids.  I’m having
> problems with longer runs.   After 600-900  ps I always get large VCM.
> I checked lipid topology and it seems ok.  Maybe there is some problem
> with my *mdp file?   Please give me some comment on this, and thank
> you in advance.
You may want to try to couple the membrane and the solvent separately. 


> 
>  
> 
> ….
> 
>            Step           Time         Lambda
> 
>          305000      610.00000        0.00000
> 
>  
> 
>    Rel. Constraint Deviation:  Max    between atoms     RMS
> 
>        Before LINCS         0.072926   5163   5166   0.025714
> 
>         After LINCS         0.000039   4759   4760   0.000009
> 
>  
> 
>    Energies (kJ/mol)
> 
>            Bond          Angle    Proper Dih. Ryckaert-Bell.  Improper
> Dih.
> 
>     8.39732e+03    1.67752e+04    6.25326e+03    3.60327e+03
> 8.99070e+02
> 
>           LJ-14     Coulomb-14        LJ (SR)   Coulomb (SR)
> Potential
> 
>     9.39095e+03   -1.99649e+04    1.75564e+04   -4.71882e+05
> -4.28971e+05
> 
>     Kinetic En.   Total Energy    Temperature Pressure (bar)
> 
>     7.62203e+04   -3.52751e+05    3.02711e+02   -6.42276e+02
> 
>  
> 
> Large VCM(group PC):    237.90714,  -2554.62744,   2074.48413, ekin-
> cm:  2.90949e+11
> 
> Large VCM(group SOL):   -110.55383,   1187.11670,   -964.00018, ekin-
> cm:  1.35202e+11
> 
> There were 2 inconsistent shifts. Check your topology
> 
> Large VCM(group PC): -144534.25000, 1364136.62500, -1206019.87500,
> ekin-cm:  8.91658e+16
> 
> Large VCM(group SOL): -23919.93359, -1180828.00000, -975466.56250,
> ekin-cm:  1.34954e+17
> 
> Large VCM(group PC):          inf,         -inf,          inf, ekin-
> cm:          inf
> 
>  
> 
>  
> 
> -------------------------------------------------------------------------
> 
> My mdp:  
> 
>  
> 
>  
> 
> ;       User spoel (236)
> 
> ;       Wed Nov  3 17:12:44 1993
> 
> ;       Input file
> 
> ;
> 
> title               =   4ns ps pe pc
> 
> cpp                 =  /lib/cpp
> 
> define              =  -DFLEX_SPC
> 
> constraints         =  h-bonds
> 
> integrator          =  md
> 
> dt                  =  0.002    ; ps !
> 
> nsteps              =  2000000  ; total 1000 ps.
> 
> nstxout             =  50000
> 
> nstvout             =  50000
> 
> nstfout             =  50000
> 
> nstlog              =  5000
> 
> nstenergy           =  1000
> 
> nstlist             =  10
> 
> ns_type             =  grid
> 
> rlist               =  1.0
> 
>  
> 
> ; Method for doing VdW
> 
> vdw-type            =  Cut-off
> 
> rvdw                =  1.0
> 
>  
> 
> ; Method for doing electrostatics
> 
> coulombtype         =  PME
> 
> rcoulomb            =  1
> 
> fourierspacing      =  0.12
> 
> fourier_nx          =  0
> 
> fourier_ny          =  0
> 
> fourier_nz          =  0
> 
> pme_order           =  4
> 
> ewald_rtol          =  1e-5
> 
> optimize_fft        =  yes
> 
>  
> 
> ; Berendsen temperature coupling is on in two groups
> 
> Tcoupl              =  berendsen
> 
> tc-grps             =  PC  PE PS   SOL Na
> 
> tau_t               =  0.1   0.1   0.1  0.1 0.1
> 
> ref_t               =  310 310 310 310 310
> 
> ; Energy monitoring
> 
> energygrps          = PC  PE PS   SOL Na
> 
> ; Isotropic pressure coupling is now on
> 
> Pcoupl              =  berendsen
> 
> Pcoupltype          = semiisotropic
> 
> tau_p               =    20         20
> 
> compressibility     =  4.5e-5    4.5e-5
> 
> ref_p               =  1.0  1.0
> 
>  
> 
>  
> 
>  
> 
>  
> 
> ; Generate velocites is off at 300 K.
> 
> gen_vel             =  yes
> 
> gen_temp            =  310.0
> 
> gen_seed            =  173529
> 
> ; Groups for center of mass motion removal
> 
> comm-grps            = PC  PE PS   SOL Na
> 
> ; Mode for center of mass motion removal
> 
> comm-mode            =  Linear
> 
> ; Center of mass control
> 
> nstcomm              =  1
> 
>  
> 
> ; Periodic boundary conditions
> 
> pbc                  =  xyz
> 
>  
> 
>          
> 
>  
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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