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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IIIT - H.
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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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