[gmx-users] Timestep

Ramya Cherukupalli ramya at research.iiit.ac.in
Tue Aug 7 13:03:11 CEST 2007


    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
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,

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