[gmx-users] problem in running md simulation

[ananyachatterjee]

 Hi all,

 As suggested by venhat I have energy minimised it till 1000Kj/mol but 
 even now I am getting the same error, saying

 Warning: 1-4 interaction between 3230 and 3233 at distance 3.573 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 = 90.674 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.

 can anyone suggest me what to do now.

 Ananya Chatterejee



  On Thu, 15 Nov 2012 11:38:17 +0530, Venkat Reddy wrote:
> 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.
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> 
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> * Please search the archive at http://www.gromacs.org/**
>> 
>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before 
>> posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read 
>> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>
>
>
>
> --
> With Best Wishes
> Venkat Reddy Chirasani
> PhD student
> Laboratory of Computational Biophysics
> Department of Biotechnology
> IIT Madras
> Chennai
> INDIA-600036

-- 
 Ananya Chatterjee,
 Department of biological Science,
 IISER-Kolkata.