[gmx-users] problem in running md simulation
Kavyashree M
hmkvsri at gmail.com
Fri Nov 16 16:10:52 CET 2012
Hi Ananya,
Can you try with rvwd 0.9nm and rcolumb with 1.4nm..?
vdw interaction decreases as 1/r^6, while columbic
interaction decreases as (1/r).. so it would be better if
you consider columbic interaction for longer distance
than vdw interaction..
bye
kavya
On Fri, Nov 16, 2012 at 8:32 PM, ananyachatterjee <
ananyachatterjee at iiserkol.ac.in> wrote:
> 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 <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
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>>>
>>
>>
>> --
>> 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.
> --
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