[gmx-users] VCM

[David van der Spoel]

On Wed, 2005-05-04 at 12:22 +0200, Michal Kolinski wrote:
> I’m running MD of lipid membrane made of three types of lipids (PS,
> PC, PE)
> I always get VCM after about 300 to 400 ps.  
> In my *.mdp file I’m using to groups lipidpcpeps and sol_ion for 
> center of mass motion removal and temperature coupling.  
> I tried using different configurations for my groups then 
> position restraints  lipids but I didn’t
> help.  What can I do to solve this problem?
>  


increase rvdw. your lipid head groups are big, roughly the size of the
cutoff, meaning they can all of a sudden be in very close contact. make
it 1.5 or so.
> 
> ---------------------------------------------------------------------------------------
> Error message in log file:
>  
>  
>  
>     Step           Time         Lambda
>           90000      180.00002        0.00000
>  
>    Rel. Constraint Deviation:  Max    between atoms     RMS
>        Before LINCS         0.048160   4236   4238   0.018847
>         After LINCS         0.000018   5223   5224   0.000004
>  
>    Energies (kJ/mol)
>            Bond          Angle    Proper Dih. Ryckaert-Bell.  Improper
> Dih.
>     1.09413e+04    1.60613e+04    5.94364e+03    3.61899e+03
> 8.39084e+02
>           LJ-14     Coulomb-14        LJ (SR)   Coulomb (SR)   Coulomb
> (LR)
>     9.19145e+03   -5.51505e+04    3.34016e+04   -4.03104e+05
> -1.55198e+05
>  Position Rest.      Potential    Kinetic En.   Total Energy
> Temperature
>     3.18901e+04   -5.01565e+05    9.08787e+04   -4.10686e+05
> 3.00361e+02
>  Pressure (bar)
>    -5.80396e+02
> Large VCM(group lipidpcpeps): 12860086.00000, 5915031552.00000,
> 60308048.00000, ekin-cm:  1.84720e+24
>  
> -----------------------------------------------------------------------------------------
> my mdp file:
>  
> 
> title               =   blona 4ns ps pe pc
> cpp                 =  /lib/cpp
> define              =  -DFLEX_SPC
> constraints         =  hbonds
> integrator          =  md
> dt                  =  0.002    ; ps !
> nsteps              =  1000000  
> nstxout             =  20000
> nstvout             =  20000
> nstfout             =  20000
> nstlog              =  10000
> nstenergy           =  10000
> nstxtcout           =  10000
> nstlist             =  10
> ns_type             =  grid
> rlist               = 0.9
>  
> ; Method for doing VdW
> vdw-type            =  Cut-off
> rvdw                =  0.9
>  
> ; Method for doing electrostatics
> coulombtype         =  PME
> rcoulomb            = 0.9
> 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             =  sol_ion lipidpcpeps 
> tau_t               =  0.01   0.01
> ref_t               =  300  300 
> ; Energy monitoring
> energygrps          = PC  PE PS   SOL Na
>  
> ; Generate velocites is off at 300 K.
> ;gen_vel             =  yes
> gen_temp            = 300.0
> ;gen_seed            =  173529
> ; Groups for center of mass motion removal
> comm-grps            =  sol_ion lipidpcpeps
> ; 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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