On Thu, Jun 28, 2012, Fabrício Bracht wrote:
> Hi. I did what you asked. I ran the simulation again, in order to make
> sure that the error happened again. This time, it dies a lot earlier
> with the same warnings as last time (vlimit exceed....etc). I
> continued the simulation using as input the last restrt file written
> using the serial version of pmemd. The simulation crashed after a few
> hours , the last output lines are:
>
>
>
> vlimit exceeded for step 112126; vmax = 91.1788
> vlimit exceeded for step 112176; vmax = 45.6806
>
> Coordinate resetting cannot be accomplished,
> deviation is too large
> iter_cnt, my_bond_idx, i and j are : 2 2690 5315 5316
>
Thanks for the info. It looks to me like the problem has nothing to do (per
se) with GPU's, since you can reproduce it on a serial CPU using pmemd.
Unfortuantely, problems like this (generally with the force field) can be hard
to track down. Your mdin file looks fine to me, although it is safer to use
dt=0.001 rather than 0.002, especially for constant pressure simulations, and
if you system is not *quite* equilibrated.
The information above indicates that the problem occurs around atoms 5315
and 5316. You might see what those are, as this might (or might not) give
a clue to the origin of the problem. Look hard (and/or let us know about)
any non-standard residues or molecules that are in your simulation. Do
you have any Lennard-Jones rmin values that are either zero or small (i.e.
less than typical values for that type of atom)? You may have to get a
restart file someplace a little before step 112126; (don't use ig=-1 to do
this: copy the actual seed that is printed in your output file, so you will
get an identical trajectory.) Then you can set ntwx=1, and examine the
coordinates at every step as the system crashes....one hopes that this will
identify the source of the problem.
...good luck...dac
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Received on Thu Jun 28 2012 - 08:00:04 PDT
