Hi Jason,
Thanks, that's very informative. The system is a ligand-receptor complex so
the ligand is definitely an isolated molecule, diffusion is a possibility.
I am using an implicit solvent model at the moment so you are correct. I am
actually trying to do a quick MD run to see how the ligand is behaving when
in the active site to try to find hints as to why our in vivo data doesn't
even come close to my docking data even though we have an XRD of the
receptor with a known ligand bound and use that as a template.
Pmemd didnt seem to leave anything useful in the .out file except the
mention of misunderstanding of that particular line. Since I'm running it
on multicore I didn't get any stdout errors as it was seperate MPI
processes/threads. Unless there is somewhere else I can find more
information on the problem.
Otherwise I can try to build an explicit solvent model if this is more
appropriate. I'm very new to this so I'm not entirely sure what the best
way is to approach this scenario.
Cheers,
Sebastian
On 29 April 2013 10:59, Jason Swails <jason.swails.gmail.com> wrote:
> On Sun, Apr 28, 2013 at 8:17 PM, Sebastian Petrik <
> sebastian.petrik.griffithuni.edu.au> wrote:
>
> > Hello,
> >
> > I have been attempting a simple minimize-warmup-dynamics run and seem to
> be
> > running into a problem with both SANDER and PMEMD. My latest trial
> > minimizes fine, warms up fine but as the dynamics run is attempted it
> fails
> > on:
> >
> > | ERROR: I could not understand line 2597
> > 412.9567261 427.1826530-780.4936416
> >
> > Inspection of the warmup RST file shows at about 2500 lines in some
> values
> > start to get replaced with ************* which i assume is out of bounds
> > and is probably not a good thing?
> >
> > A snippet of the lines around 2597 is provided below, which I hope
> someone
> >
> > can make sense of. It looks as if it might be truncated?
> >
>
> The issue is that the formatted restart file uses a fixed number of
> characters in 12.7 precision (12 total characters with 7 decimal places).
> Therefore, there is not enough space to represent numbers -1000 and lower
> or 10000 and higher.
>
> This can happen when you have systems comprised of multiple molecules that
> are not connected by bonds, and these molecules naturally diffuse and drift
> away from each other. This is typical for explicit solvent calculations,
> only, since implicit solvent calculations are infinitely dilute (and the
> lack of explicit solvent molecules means diffusion is impossible to model).
>
> For explicit solvent calculations, there are two solutions: use NetCDF
> restart files (Amber 12 or later, I believe), which can accommodate any
> double precision value (not just those between -1000 and 10000). The
> second is to use the iwrap=1 variable so that all particles that diffuse
> out of the 'main' unit cell are 'wrapped' back into the 'main' unit cell on
> the other side.
>
> It typically takes a very long time for these particles to diffuse far
> enough away to cause these types of errors (but with GPUs becoming more
> common, this issue pops up more). The fact that this is happening in your
> heating phase leads me to believe that you are doing this in implicit
> solvent, and that you have numerous molecules that are not interconnected.
> In this case, you will need to find a way to prevent this kind of particle
> diffusion. You can either jump to explicit solvent, or you can use some
> kind of restraint system (but think about the questions you are asking and
> how these simulations will be able to answer those questions).
>
> HTH,
> Jason
>
> P.S., Did you not get a helpful message from pmemd when you got this error?
> You hopefully saw something similar to this email...
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Sun Apr 28 2013 - 19:00:02 PDT
