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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