Just to add: I did run the minimization using the CPU code of AMBER and
then tried to switch to the GPU code.
On Mon, Feb 6, 2023 at 3:24 PM Prithviraj Nandigrami <
prithviraj.nandigrami.gmail.com> wrote:
> Dear AMBER Experts,
>
> I am encountering the following error during the equilibration/production
> stage of a simulation of nucleic acid. The minimization runs fine but
> during the equilibration, it exits with an error message:
>
>
> Error: an illegal memory access was encountered launching kernel
> kClearForces
> ERROR: Calculation halted. Periodic box dimensions have changed too much
> from their initial values.
> Your system density has likely changed by a large amount, probably from
> starting the simulation from a structure a long way from equilibrium.
>
> [Although this error can also occur if the simulation has blown up for
> some reason]
>
> The GPU code does not automatically reorganize grid cells and thus you
> will need to restart the calculation from the previous restart file.
> This will generate new grid cells and allow the calculation to continue.
> It may be necessary to repeat this restarting multiple times if your
> system
> is a long way from an equilibrated density.
>
> Alternatively you can run with the CPU code until the density has
> converged
> and then switch back to the GPU code.
>
> Now, when I look at the equilibration output files, I do not see anything
> obviously amiss. Additionally, cpptraj "checkstructure" did not show any
> clashes that may be occuring.
> I attached the minimization and equilibration output files. Also, here are
> the input files I am using.
>
> *Minimization*
>
> Minimization input file in explicit solvent
> &cntrl
> ! Minimization options
> imin=1,
> maxcyc=20000,
> ncyc=2500,
>
> ! Potential energy function options
> cut=12.0,
>
> fswitch=10.0,
>
> ! Control how often information is printed to the output file
> ntpr=1,
> ntxo=2,
>
> ! Restraint options
> ntr=1,
>
> ! Set water atom/residue names for SETTLE recognition
> watnam='WAT',
> owtnm='O',
> /
>
> &ewald
> vdwmeth = 0,
> /
> RNA posres
> 1.0
> RES 1 65
> END
> END
>
> *Equilibration*
>
> A NVT simulation
> &cntrl
> imin=0,
> irest=0,
> ntx=1,
>
> ! Temperature control
> ntt=3,
> gamma_ln=1.0,
> tempi=300.0,
> temp0=300.0,
>
> ! Potential energy control
> cut=12.0,
> fswitch=10.0,
>
> ! MD settings
> nstlim=500000,
> dt=0.001,
>
> ! SHAKE
> ntc=2,
> ntf=2,
>
> ! Control how often information is printed
> ntpr=1000,
> ntwx=5000,
> ntwr=10000,
> ntxo=2,
> ioutfm=1,
>
> ! Wrap coordinates when printing them to the same unit cell
> iwrap=0,
>
> ! Restraint options
> ntr=1,
>
> ! Set water atom/residue names for SETTLE recognition
> watnam='WAT',
> owtnm='O',
> /
>
> &ewald
> vdwmeth = 0,
> /
> Protein posres
> 1.0
> RES 1 65
> END
> END
>
> *Production*
>
> A NPT simulation
> &cntrl
> imin=0,
> irest=1,
> ntx=5,
>
> ! Temperature control
> ntt=3,
> gamma_ln=1.0,
> temp0=300.0,
>
> ! Potential energy control
> cut=12.0,
> fswitch=10.0,
>
> ! MD settings
> nstlim=10000000,
> dt=0.002,
>
> ! SHAKE
> ntc=2,
> ntf=2,
>
> ! Control how often information is printed
> ntpr=1000,
> ntwx=50000,
> ntwr=10000,
> ntxo=2,
> ioutfm=1,
>
> ! Wrap coordinates when printing them to the same unit cell
> iwrap=1,
>
> ! Constant pressure control.
> barostat=1,
> ntp=1,
> pres0=1.0,
>
> ! Set water atom/residue names for SETTLE recognition
> watnam='WAT',
> owtnm='O',
> /
>
> &ewald
> vdwmeth = 0,
> /
>
>
> I would appreciate any help.
>
> Thank you.
> PN
>
>
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Received on Mon Feb 06 2023 - 13:00:03 PST
