[gmx-users] problem in running md simulation

[Venkat Reddy]

I think the system is not well energy minimized. Do it for 1000kj/mol. Also
check for bad contacts in your starting structure using Ramachandran plot.
One more important thing is that, you have to generate an index file with
Protein_GTP as one group and water_Ions as another. Then change your
 tc-groups as

tc-grps     = Protein_GTP   Water_Ions
tau_t       =      0.1         0.1     ; time constant, in ps
ref_t       =       300       300


On Thu, Nov 15, 2012 at 10:50 AM, ananyachatterjee <
ananyachatterjee at iiserkol.ac.in> wrote:

> 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.
> --
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-- 
With Best Wishes
Venkat Reddy Chirasani
PhD student
Laboratory of Computational Biophysics
Department of Biotechnology
IIT Madras
Chennai
INDIA-600036