[gmx-users] Langevin dynamics ( Large VCM )

[Dongsheng Zhang]

If you want to use BD, the friction coefficient has to be large. Please
check the manual. If you change your bd-fric to 5000, it might help.



 On Wed, 2006-08-02 at 23:24 +0800, PAUL NEWMAN wrote:
> Hi:
> Thanks to everybody who helped me out with my last email. But now I
> have another problem and I hope you can help me. As i told you I'm
> doing a simulation of polyelectrolyte chain consisting of 50 charged
> beads (-1) with 50 charged counterions(+1). My box simulation is 400
> nm x 400 nm x 400 nm  and the polyelectrolyte length is 100 nm. My
> problem is when I chage the intregator md to bd (position langevin
> dynamics), it  gives me  Large VCM (group System) in the md.log file
> and after some time it crashes at some point. When i take a look at
> the energy file and plot the temperature I realized that the
> temperature is far from the desired temperature. Please take a look at
> my mdp file and help me figure out what i'm doing wrong. 
> My last question how can I choose the rlist, Vdw and coulomb  cut-off
> when  I'm using PME and , for example my case in   400 nm x 400 nm x
> 400 nm and 100 atoms with fourierspacing = 20 (is it ok?). Thanks in
> advance.
> ;	By user: pcl
> ; VARIOUS PREPROCESSING OPTIONS
> title                    = Yo
> cpp                      = /lib/cpp
> include                  = 
> define                   = 
> 
> ; RUN CONTROL PARAMETERS
> 
> integrator               = bd
> ; Start time and timestep in ps
> tinit                    = 0
> dt                       = 0.0001
> nsteps                   = 100000000
>                     
> comm-mode                = Linear 
> 
> nstcomm                  = 1
> comm-grps                = System
> 
> ; LANGEVIN DYNAMICS OPTIONS
> ; Friction coefficient (amu/ps) and random seed
> bd-fric                  = 0.05 
> ld_seed                  = 1993
> 
> 
> ; NEIGHBORSEARCHING PARAMETERS
> ; nblist update frequency
> nstlist                  = 10 ;
> ; ns algorithm (simple or grid)
> ns_type                  = grid
> ; Periodic boundary conditions: xyz (default), no (vacuum)or full (infinite systems only)
> 
> pbc                      = xyz
> ; nblist cut-off        
> rlist                    = 100
> 
> ; OPTIONS FOR ELECTROSTATICS AND VDW
> ; Method for doing electrostatics
> coulombtype              = PME
> ;rcoulomb-switch          = 0
> 
> rcoulomb                 = 100
> fourierspacing           = 20
> optimize_fft             = yes
> ; Relative dielectric constant for the medium and the reaction field
> epsilon_r                = 13.89354;  
> ; Method for doing Van der Waals
> 
> vdw-type                 = Cut-off      
> rvdw-switch              = 0
> rvdw                     = 100
> 
> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
> ; Temperature coupling  
> Tcoupl                   = Berendsen
> 
> ; Groups to couple separately
> tc-grps                  = NA POL
> ; Time constant (ps) and reference temperature (K)
> tau_t                    = 0.01  0.01
> ref_t                    = 120.2717 120.2717; 
> 
> 
> ; Pressure coupling     
> Pcoupl                   = no
> 
> ; GENERATE VELOCITIES FOR STARTUP RUN
> gen_vel                  = no
> 
> ; OPTIONS FOR BONDS    
> constraints              = none
> 
> -- 
> Cheers,    
>       
> Paul 
> National Tsing Hua University (清A大W)
> 
> xx你的兔
> I appreciate your help. Thanks!
> Os agradezco la ayuda. Gracias! 
> 
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