[gmx-users] MD problem with nwall=2

김현식 nammika at hotmail.com
Wed Sep 5 13:28:30 CEST 2012

Dear Experts
I have tried to run md simulation with wall option, which included "nwall=2". However, there have been some problems. Always, the running is down with no error message or a message like below.
-------------------------------------------------------Program mdrun_mpi_d, VERSION 4.5.3Source code file: ns.c, line: 2544
Fatal error:One of the box vectors has become shorter than twice the cut-off length or box_yy-|box_zy| or box_zz has become smaller than the cut-off.For more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors-------------------------------------------------------
And at this point, my triclinic system was getting larger in both Z-directions, and was getting smaller in X and Y directions.In my thinking, it may be happen because of changing the box. Can anyone who have experience like that or how to handle this give me some advise?
I attach some parts of my mdp file to run md.  ; Temperature coupling is on tcoupl          = V-rescale     ; modified Berendsen thermostat tc-grps         = Protein Non-Protein   ; two coupling groups - more accurate tau_t           = 0.1   0.1     ; time constant, in ps ref_t           = 300   300     ; reference temperature, one for each group, in K   ; Pressure coupling is on pcoupl          = Berendsen     ; Pressure coupling on in NPT pcoupltype      = semiisotropic     ; uniform scaling of box vectors tau_p           = 2.0 2.0          ; time constant, in ps ref_p           = 1.0 1.0          ; reference pressure, in bar compressibility = 4.5e-5 4.5e-5       ; isothermal compressibility of water, bar^-1   ; Periodic boundary conditions pbc             = xy           ; 2-D PBC   
 ;Wall nwall           = 2             ;  wall_type    = 9-3    wall_r_linpot    = 1   wall_atomtype   =  opls_001 opls_001    wall_density    = 20 20   wall_ewald_zfac    = 3 ewald_geometry  = 3dc           ;

Thank youHyunsik 		 	   		  

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