AMBER Archive (2008)

Subject: AMBER: NAN errors in Etot, EPtot, EKtot and EELEC

From: Praveena Gopal (
Date: Thu Jun 05 2008 - 07:04:00 CDT

Dear Amber Users,
         I'm trying to run 20ps initial MD with dt of 0.002ps for a cyclic hexapeptide dimer solvated in water using Amber version 8. I've kept the dimer fixed with a small restraint of 10kcal/molA2. The output seems to have NAN errors for ETOT, EKTOT, EPTOT amd EELEC values. I've searched in mailing lists and found few mails regarding that. But unfortunately could not find a solution with what is given. Kindly let me know what could be the reason for NAN errors. How could I recover from that?
  I've checked the dimer in xleap which seems to be ok in both isolated and solvation forms. I've also tried reducing the restraint on solute and by turning off the shake. Now the run continues without any NAN error but with vilimt exceeding in every steps. However after few steps the program terminates automatically with following messages:
  "Frac coord min, max: -7.13960686514676458E-6, 0.70635552688012537
   The system has extended beyond
       the extent of the virtual box.
   Restarting sander will recalculate
      a new virtual box with 30 Angstroms
      extra on each side, if there is a
      restart file for this configuration.
   SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
   Atom out of bounds. If a restart has been written,
   restarting should resolve the error
  As it shows restart would solve the problem, I've tried restarting the program. Though it ran for few steps (with vilimt exceeding in every steps), program then aborted with the same messages.
  Herewith I have attached the dt=0.001.out and dt=0.002.out files.
  Kindly suggest an idea to rectify.
  Thanks in advance.


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)