[gmx-users] VCM

[Michal Kolinski]

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.

 

..

           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

 

         

 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20050404/f1b785ea/attachment.html>