[gmx-users] problem in running md simulation

[ananyachatterjee]

 Hi all,

 I was running a md simulation of protein complexed with GTP in water, 
 neutralised with Mg2+ and Cl- ions.I have also em the system to 
 2000kj/mol and also equilibrated the water molecules in 300K temperature 
 and 1 bar pressure. And then run the md simulation using md parameters 
 as follow:

 title       = Protein-ligand complex
 ; Run parameters
 integrator  = md        ; leap-frog integrator
 nsteps      = 500000   ; 2 * 5000000 = 1000 ps (1 ns)
 dt          = 0.002     ; 2 fs
 ; Output control
 nstxout     = 500      ; save coordinates every 1ps
 nstvout     = 500       ; save coordinates every 1ps
 nstenergy   = 500      ; save energies every 1 ps
 nstlog      = 500      ; update log file every 1 ps
 nstxtcout   = 500      ; write .xtc trajectory every 1 ps
 energygrps  = Protein GTP SOL MG2+
 ; Bond parameters
 constraints     = none    ; No constrains
 ; Neighborsearching
 ns_type     = grid      ; search neighboring grid cells
 nstlist     = 5         ; 10 fs
 rlist       = 0.9       ; short-range neighborlist cutoff (in nm)
 rcoulomb    = 0.9       ; short-range electrostatic cutoff (in nm)
 rvdw        = 1.4       ; short-range van der Waals cutoff (in nm)
 ; Temperature coupling
 tcoupl      = v-rescale                  ; modified Berendsen 
 thermostat
 tc-grps     = Protein GTP   SOL  MG2+  CL-    ; two coupling groups - 
 more accurate
 tau_t       = 0.1     0.1   0.1  0.1  0.1     ; time constant, in ps
 ref_t       = 300     300   300  300  300    ; reference temperature, 
 one for each group, in K
 ; Pressure coupling
 pcoupl      = Parrinello-Rahman             ; pressure coupling is on 
 for NPT
 pcoupltype  = isotropic                     ; uniform scaling of box 
 vectors
 tau_p       = 2.0                           ; time constant, in ps
 ref_p       = 1.0                           ; reference pressure, in 
 bar
 compressibility = 4.5e-5                    ; isothermal 
 compressibility of water, bar^-1
 refcoord_scaling    = com
 ; Periodic boundary conditions
 pbc         = xyz       ; 3-D PBC
 

 Now I am getting the following error.


 Warning: 1-4 interaction between 3231 and 3234 at distance 10.730 which 
 is larger than the 1-4 table size 2.400 nm
 These are ignored for the rest of the simulation
 This usually means your system is exploding,
 if not, you should increase table-extension in your mdp file
 or with user tables increase the table size

 t = 226.610 ps: Water molecule starting at atom 236548 can not be 
 settled.
 Check for bad contacts and/or reduce the timestep.
 Wrote pdb files with previous and current coordinates

 -------------------------------------------------------
 Program mdrun, VERSION 4.0.7
 Source code file: ../../../../src/mdlib/nsgrid.c, line: 348

 Fatal error:
 Number of grid cells is zero. Probably the system and box collapsed.

 kindly help me I am not getting where I am getting wrong.



-- 
 Ananya Chatterjee,
 Senior Research Fellow (SRF),
 Department of biological Science,
 IISER-Kolkata.