AMBER Archive (2008)

Subject: Re: AMBER: NAN errors still exist

From: Carlos Simmerling (
Date: Fri Jun 06 2008 - 05:57:49 CDT

what are you trying to simulate? there is no GB or electrostatic energy.
if it's something unusual, then as I said before you should think about
whether there could be a problem in the parameters.

On Fri, Jun 6, 2008 at 5:56 AM, Praveena Gopal <> wrote:
> 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.
> PraveenaG
> 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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Carlos L. Simmerling, Ph.D.
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