[gmx-users] problem in running md simulation
Justin Lemkul
jalemkul at vt.edu
Fri Nov 16 16:22:21 CET 2012
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> 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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>>>>>
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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
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