[gmx-users] VCM

[Erik Lindahl]

Hi,

To expand on David's explanation; the problem is likely that your  
membrane is moving in one direction and the solvent in the other. This  
is an artefact of the fairly small simulation cells used in combination  
with PBC.

Recent versions of Gromacs can remove center-of-mass velocity  
separately for multiple groups.

If you've already performed a large simulation and are having problems  
with the analysis you can partly correct for it by removing the average  
motion of the lipid group.

Cheers,

Erik



On Apr 4, 2005, at 9:02 PM, David wrote:

> 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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