Hi,
Thank both of you for your replies. But I couldn't visualize the system
after the minimization since the minimization restart file has values of
*********** in those lines where the errors occurred. Do you think a longer
minimization can solve this?
Thank you,
Olivia
On Fri, Jul 26, 2013 at 5:15 AM, Jason Swails <jason.swails.gmail.com>wrote:
> On Thu, Jul 25, 2013 at 2:45 PM, Meekyum Olivia Kim <olivijuly.gmail.com
> >wrote:
>
> > Hello,
> >
> > I'm trying to do umbrella sampling in implicit solvent with distance
> > restraint to calculate the PMF while pulling out the ligand from the
> > protein. I'm doing minimization with the adjusted distance between the
> > ligand and the receptor center of mass defined in the restraint file,
> > without SHAKE, then followed by two equilibration with SHAKE turned on.
> The
> > first equilibration fixes the protein with a small force constant. But
> the
> > first equilibration didn't start and I got this error message regardless
> of
> > the distance between the ligand and protein:
> >
> >
> > | ERROR: I could not understand line 190
> > 13.2773028 9.5137563 26.5189041************ 404.8478369************
> >
> > *s in the inpcrd file often indicate an overflow of the Fortran format
> used
> > to store coordinates in the inpcrd/restart files. This often happens when
> > particles diffuse very far away from each other. Make sure you are
> removing
> > center-of-mass translation (nscm /= 0) or check if you have multiple,
> > mobile
> > molecules that have diffused very far away from each other. This
> condition
> > is
> > highly unusual for non-periodic simulations.
> >
>
> This is a very detailed error message that gives you several possible
> explanations about why this error occurred. In fact, I wrote this error
> message based on replies that you would typically get if you asked about
> the cryptic error message "Error during floating point read" on this list.
>
> GB simulations should NOT have multiple molecules, unless they are
> non-covalently bound. Otherwise this error will occur with a long enough
> simulation.
>
> I second Levi's suggestion that you should visualize your system.
> Visualization often yields good clues about what went wrong.
>
> Good luck,
> Jason
>
> P.S. Please wait at least a couple days before reposting your question.
> People will respond as they have time (and it may take a couple days for a
> knowledgeable person to get to your question).
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Fri Jul 26 2013 - 10:00:04 PDT
