[gmx-users] problem in running md simulation
Kavyashree M
hmkvsri at gmail.com
Fri Nov 16 17:03:55 CET 2012
Oh, I am sorry That is right. But its difficult
to find The specific cutoff values to be used
for different protocols of cutoff, switch and shift..
different values are stated in different papers..
And original force field paper (eg OPLSAA) does
not explicitly specify these values.
Any references regarding this will be helpful for
the users.
bye
kavya
On Fri, Nov 16, 2012 at 8:52 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> On 11/16/12 10:10 AM, Kavyashree M wrote:
>
>> 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..
>>
>>
> One should not make haphazard changes to cutoffs. They are part of the
> force field. Changing them without basis can invalidate the force field
> model.
>
> -Justin
>
> bye
>> kavya
>>
>> On Fri, Nov 16, 2012 at 8:32 PM, ananyachatterjee <
>> ananyachatterjee at iiserkol.ac.**in <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<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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> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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