Hi Ashutosh,
> This problem occur both with GPU (Amber11) and CPU(Amber10) code. In
The fact this happens on both the CPU and GPU code pretty much confirms it
is a problem with your system. I would suggest running with just the CPU
code until you figure out what is going wrong.
Try a run with ntpr=10 and ntwx=10 and then watch it carefully to see what
happens. You should be able to see the system blowing up or something
similar happening. It would also be useful to see the energies from your
output file at the beginning and the few steps before it crashes. Chances
are you have a large VDW energy, you are also probably getting a large
temperature. The other thing might be some kind of hydroxyl collapse onto a
phosphate. This can happen occasionally since the hydroxyl hydrogens do not
have an VDW radii.
> &cntrl
> imin = 0, irest = 1, ntx=5, ntb=2, ntp = 1,
> taup=2.0, cut = 10, ntc = 2, ntf = 2, tempi = 295.0,
> temp0 = 300.0, ntt = 3, gamma_ln = 1.0, nstlim = 2500, dt = 0.001,
> ntpr =2500, ntwx = 2500, ntwr = 5000
> /
>
> In CPU with Amber 10 job stops around 87 to 97ps saying ERROR: max
> pair
> list cutoff must be less than unit cell max sphere radius! where as in
But the above input file is just for 5ns?
Note you also do NOT set ig=-1 which is HIGHLY recommended for running any
simulations but REQUIRED for ntt=3. You should ALWAYS change the random seed
before running. In fact I suspect this is your problem since you are
restarting so often. I suggest you read the following paper before
proceeding:
Cerutti, Duke, et al., "A Vulnerability in Popular Molecular Dynamics
Packages Concerning Langevin and Anderson Dynamics", J Chem Theory and
Computation 4, 1669 (2008).
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Thu Oct 27 2011 - 10:30:04 PDT
