AMBER Archive (2008)

Subject: AMBER: NAN errors still exist

From: Praveena Gopal (
Date: Fri Jun 06 2008 - 04:56:58 CDT

  Dear Simmerling,

                 As you said, I have tried to run MD by setting the initial temperature as 200 K and even 250 and 300 K. However the previous problem still persists in all the cases. Also I have tried shake with on and off state. Herewith I have attached the dt=0.001.out and dt=0.002.out files, which I have got by changing the initial temperature.
     Also I have tried running GB solvation for 50ps. But total energy and EPtot of the system seems to be positive! in the output (attached: gbeq.out). Would there be any problem with the structure. What could be done further to succesfully run MD, especially in explicit water.
     Kindly help.

     Thanks in advance.


Carlos Simmerling <> wrote: try assigning an initial temperature (tempi) other than 0.
maybe 200K or so. I find that setting tempi=0 and then using
temp0=300 causes extremely rapid heating and instability.
also 10 kcal/molA^2 is a very large restraint, not a small one.
probably not the problem here, but I just wanted to mention that.
does the dimer work if you use GB solvation? that might help
to know if it is somehow the solvation or if it is the solute.
anything unusual in the peptide- did you use only standard
force field parameters?

On Thu, Jun 5, 2008 at 8:04 AM, Praveena Gopal wrote:
> 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.
> PraveenaG
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