This looks like a problem with the simulation initialization that
ultimately leads to the system flying out of control, which in turn
generates excessively large forces and then sends particles into oblivion,
which ultimately (I think, just my hunch) leads to memory errors in the
non-bonded pairs computation. But those details are not entirely
relevant--the important thing is that this sort of error can be generated
under many circumstances, including bugs in the code that improperly
allocate or reference memory, but in this case I think it's an issue of the
system behaving badly and exceeding the reasonable bounds that the code is
designed to operate within. What does the final snapshot of the
equilibrium MD simulation look like? The BOND, ANGLE, DIHEDRAL, and all
non-bonded energies of the initial aMD snapshot look to be roughly in line
with the unbiased simulation averages. What differs wildly is the initial
Etot, which seems to be in part due to a different EKtot (30,000 kcal/mol
injected there) but much more due to an obscenely large EAMD_BOOST energy.
My feeling is that the EAMD_BOOST is just off the scale, and this generates
very high initial accelerations which in turns throws off the total kinetic
energy. The rest is history--things get yanked wildly into one another and
eventually the train wreck goes fully off the rails.
Are you using Amber16 or the new Amber18? My suspicion is that the bug is
somewhere in the aMD parameter setup, not the code per se, so if that's
true you'd be getting the same errors with either package.
Dave
On Fri, Apr 20, 2018 at 5:59 PM, Ashutosh Shandilya <scfbioiitd.gmail.com>
wrote:
> Dear Amber Users,
>
> I ran MD simulation for 10 ns and then tried to run aMD with following
> parameters
> ---------------------------------------------------------
> Accelerated MD - explicit solvent
> &cntrl
> imin=0, irest=0, ntx=1, nstlim=25000000, dt=0.002, iwrap=1,
> ntb=2, cut=10.0, ntp=1, ntc=2, ntf=2, tempi=300.0, temp0=300.0,
> ioutfm=1, ntt=3, gamma_ln=1.0, ig=-1, iamd=1,
> EthreshP=-152417, alphaP=13330, barostat=2, ntpr=5000, ntwr=5000,
> ntwx=5000
> &end
> -------------------------------------------------------------------------
>
> I encountered with this error while running aMD. My normal MD simulation
> run to get parameters also ran with pmemd.cuda which ran fine. Here is the
> final output file for that.
>
>
>
> A V E R A G E S O V E R 1000 S T E P S
>
>
> NSTEP = 5000000 TIME(PS) = 10100.0 TEMP(K) = 299.95 PRESS
> = -1.5
> Etot = -302570.25 EKtot = 73158.56 EPtot =
> -375728.8244
> BOND = 2365.12 ANGLE = 6165.20 DIHED = 9862.4871
> 1-4 NB = 2781.82 1-4 EEL = 21490.98 VDWAALS = 43693.4265
> EELEC = -462087.88 EHBOND = 0.00 RESTRAINT = 0.0000
> EKCMT = 32326.40 VIRIAL = 32365.48 VOLUME = 1192465.2387
> Density = 1.0238
> ------------------------------------------------------------
> ------------------
>
> Visual inspection of the pdb structure generated from rst file also looks
> normal.
>
>
> Although, I am not sure why aMD output file shows higher temperature at the
> first step
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) =
> *437.64*
> PRESS = 0.0
> Etot = -58253.34 EKtot = 106742.86 EPtot =
> -164996.20
> BOND = 2353.15 ANGLE = 6119.93 DIHED =
> 9847.52
> 1-4 NB = 2754.62 1-4 EEL = 21776.16 VDWAALS =
> 43983.47
> EELEC = -462590.85 EHBOND = 0.00 RESTRAINT =
> 0.00
> EAMD_BOOST = 210759.76
> EKCMT = 0.0000 VIRIAL = 0.00 VOLUME = 1192520.97
> Density = 1.0238
> -----------------------------------------------------------------
>
> Could any one suggest possible solution?
>
> Many thanks,
>
> Ash
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Received on Fri Apr 20 2018 - 20:30:02 PDT
