[gmx-users] VCM

[Michal Kolinski]

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?


---------------------------------------------------------------------------------------
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

----------------------------------------------------------------------------
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20050504/e46bbda4/attachment.html>