ramya at research.iiit.ac.in
Tue Aug 7 19:22:01 CEST 2007
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..
> 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.
>> 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
>> time.But this'll be time consuming.I am unable to figure out any
>> 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,
>> 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
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