[gmx-users] Timestep

[Ramya Cherukupalli]

Thank a lot to all for your inputs..

Ramya.


> Hi,
>
> In principle Gromacs should never just crash with a segmentation
> fault, but at least give you a (perhaps cryptic) error message and
> exit somewhat gracefully.
>
> As far as I know there is only one exception to this: If you are
> using tabulated interactions the table can only be of finite size,
> and thus there will be a cutoff beyond which there is no data.
> Unfortunately it is not possible to determine this automatically, so
> you have to set the table extension beyond your normal cutoffs in the
> mdp file (table-ext).   The obvious question is of course why we
> don't do a check for the distance before the table lookup, but that
> would be a conditional statement in the very innermost nonbonded
> loop, and drastically reduce performance.
>
> I don't think your system will explode completely with 3fs steps
> though, so the best options might be to compile with debug flag (./
> configure CFLAGS="-O3 -g") and run the simulation in a debugger to
> see where it crashes.
>
> Cheers,
>
> Erik
>
>
> On Aug 7, 2007, at 8:30 PM, Xavier Periole wrote
>
>>
>> It is not possible to answer your question from the information you
>> give.
>> A lot of things can cause a segmentation fault. From compilation to
>> your particular system. Put a search on the user-list, you'll get
>> an idea
>> of possible problems.
>>
>> It depends what you will be looking at but I would suggest to stick
>> to a 2 fs time step.
>>
>> XAvier
>>
>>>  Thanks to Xavier for his prompt reply..
>>>  Actually my objective is a bit longer[50-60ns] but the problem is
>>> that
>>> even if i cant change the time-step to 0.003 it is exiting saying
>>> segmentation fault then how is it possible with 1fs [or 4 fs as
>>> suggested] which i want to do to reduce time.
>>>  I wanted to know where the problem is... why cant i increase the
>>> time
>>> step and the only error shown is 'segmentation fault'..so is the
>>> reason
>>> in compilation or coding or machine precision or is it with molecular
>>> system wise thats what i was trying to understand..
>>> Thanks again..
>>> Ramya.
>>>>
>>>> 10 ns of a solvated protein of regular size should not require much
>>>> computing time.
>>>>
>>>> Increasing the time-step above 2 fs is a solution to increase the
>>>> speed of the run but then you face the problem of not integrating
>>>> the fast movement correctly and this can end up in large forces
>>>> and then you run crashes.
>>>> You could use dummy hydrogens (see manual) and heavy water and
>>>> use a 4 fs time step. This is ok for a simple protein in a box
>>>> of water.
>>>>
>>>> But again 10ns of a protein solvated is not a long simulation.
>>>>
>>>> XAvier
>>>>>
>>>>>    I am trying to perform a simulation run of 10ns for my system
>>>>> [protein+waterbox].The system works fine if i use timestep[dt=0.002
>>>>> fs].   To balance the run time and time-consumption, when we try a
>>>>> .mdp file with slight increase of timestep i.e., to 0.003 fs;
>>>>> grompp
>>>>> works fine and generates input tpr, but when going further with
>>>>> mdrun,
>>>>> the program crashes, giving error:
>>>>>     "Segmentation Fault"
>>>>>
>>>>> So i have to increase the number of steps[nsteps] to achieve
>>>>> required
>>>>> run
>>>>> time.But this'll be time consuming.I am unable to figure out any
>>>>> alternative.
>>>>> I am using Gromacs 3.3 on IBM Power5 machine with SLES9.
>>>>> Please suggest me the required to be done.Thanks in advance.
>>>>>
>>>>> The .mdp file i've used:
>>>>>
>>>>> integrator               = md
>>>>> ;Total simulation time: 5000 ps
>>>>> :time step in femtoseconds
>>>>> dt                       = 0.002
>>>>> ;number of steps
>>>>> nsteps                   = 2500000
>>>>> nstxout                  = 100
>>>>> nstvout                  = 100
>>>>> nstlog                   = 10
>>>>> nstenergy                = 10
>>>>> nstxtcout                = 10
>>>>> ;xtc_grps                = prot
>>>>> ;group(s) to write to energy file
>>>>> energygrps               = protein non-protein
>>>>> Frequency to update the neighbor list (and the long-range forces,
>>>>> ;when using twin-range cut-off's).
>>>>> nstlist                  = 10
>>>>> cut-off distance for the short-range neighbor list
>>>>> rlist                    = 0.8
>>>>> ;treatment of electrostatic interactions
>>>>> coulombtype              = PME
>>>>> rcoulomb                 = 0.9
>>>>>
>>>>>
>>>>>
>>>>> *********$$$*********
>>>>>
>>>>> Ramya Cherukupalli,
>>>>> Final year,
>>>>> M.S Bioinformatics,
>>>>> IIIT - H.
>>>>>
>>>>>
>>>>> --
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>>>>
>>>> -----------------------------------------------------
>>>> XAvier Periole - PhD
>>>>
>>>> 1- Institute of Molecular Assemblies
>>>>       City University of New York - USA
>>>> 2- Molecular Dynamics-Group
>>>>       University of Groningen - The Netherlands
>>>> http://md.chem.rug.nl/~periole
>>>> -----------------------------------------------------
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>>>>
>>> *********$$$*********
>>> Ramya Cherukupalli,
>>> Final year,
>>> M.S Bioinformatics,
>>> IIIT - H.
>>> --
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>>
>> -----------------------------------------------------
>> XAvier Periole - PhD
>>
>> 1- Institute of Molecular Assemblies
>>      City University of New York - USA
>> 2- Molecular Dynamics-Group
>>      University of Groningen - The Netherlands
>> http://md.chem.rug.nl/~periole
>> -----------------------------------------------------
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*********$$$*********

Ramya Cherukupalli,
Final year,
M.S Bioinformatics,
IIIT - H.


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