Dear Experts,
Specifically, this is the error message I am getting:
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.
I am running the minimization, heating, equilibration, and production
stages as follows:
srun --gres=gpu:1 /usr/local/bio/amber20/bin/pmemd -O -i mini.in -o
mini.out -p input_methylated.solvated.prmtop -c
input_methylated.solvated.rst7 -r mini.rst7 -inf mini.mdinfo -ref
input_methylated.solvated.rst7
srun --gres=gpu:1 /usr/local/bio/amber20/bin/pmemd.cuda -O -i heat.in -o
heat.out -p input_methylated.solvated.prmtop -c mini.rst7 -r heat.rst7 -inf
heat.mdinfo -x heat.mdcrd -ref mini.rst7
srun --gres=gpu:1 /usr/local/bio/amber20/bin/pmemd.cuda -O -i eq.in -o
eq.out -p input_methylated.solvated.prmtop -c heat.rst7 -r eq.rst7 -inf
eq.mdinfo -x eq.mdcrd -ref heat.rst7
srun --gres=gpu:1 /usr/local/bio/amber20/bin/pmemd.cuda -O -i md.in -o
md.mdout -p input_methylated.solvated.prmtop -c md.rst7 -r md.rst7 -inf
md.mdinfo -x md.nc
Also, the input files look like this:
*mini.in <
http://mini.in>*
Minimzing the system
with 25 kcal/mol restraints
on RNA, 500 steps of steepest
descent and 500 of
conjugated gradient
&cntrl
imin=1,
ntx=1,
irest=0,
ntpr=50,
ntf=1,
ntb=1,
cut=9.0,
nsnb=10,
ntr=1,
maxcyc=10000,
ncyc=5000,
ntmin=1,
restraintmask=':1-67',
restraint_wt=25.0,
&end
&ewald
ew_type = 0, skinnb = 5.0,
&end
*heat.in <
http://heat.in>*
Heating the system with 25 kcal/mol
restraints on RNA, V=const
&cntrl
imin=0, ntx=1, ntpr=500,
ntwr=500, ntwx=500, ntwe=500,
nscm=5000,
ntf=2, ntc=2,
ntb=1, ntp=0,
nstlim=1000000, t=0.0, dt=0.002,
cut=9.0,
tempi=100.0, ntt=1,
ntr=1,nmropt=1,
restraintmask=':1-67',
restraint_wt=25.0,
&end
&wt type='TEMP0',istep1=0,
istep2=5000, value1=100.0,value2=300.0,
&end
&wt type='TEMP0',istep1=5001,
istep2=50000, value1=300.0,value2=300.0,
&end
&wt type='END', &end
*eq.in <
http://eq.in>*
Equilibrating the system
with 0.5 kcal/mol restraints
on RNA, during 500ps, at
constant T= 300K & P=1ATM
and coupling = 0.2
&cntrl
imin=0, ntx=5, ntpr=500,
ntwr=500, ntwx=500,
ntwe=500,
nscm=5000,
ntf=2, ntc=2,
ntb=2, ntp=1, tautp=0.2,
taup=0.2,
nstlim=1000000,
t=0.0, dt=0.002,
cut=9.0,
ntt=1,
ntr=1,
irest=1,
restraintmask=':1-67',
restraint_wt=0.5,
&end
&ewald
ew_type = 0, skinnb = 5.0,
&end
*md.in <
http://md.in>*
production
&cntrl
imin=0, ntx=5,
ntpr=1000,ntwr=1000,
ntwx=1000,ntwe=1000,
nscm=1000,
ntf=2, ntc=2,
ntb=2, ntp=1, tautp=5.0, taup=5.0,
nstlim=10000000, t=0.0, dt=0.002,
cut=9.0,
ntt=1,
irest=1,
iwrap=1,
ioutfm=1,
&end
&ewald
ew_type = 0, skinnb = 5.0,
&end
I tried applying different restraints and/or using a smaller/larger water
box dimension but to no avail. Running the minimization using the CPU code
does not help either.
Any help/guidance would be much appreciated.
Best regards,
PN
On Thu, Jan 12, 2023 at 4:14 PM Prithviraj Nandigrami <
prithviraj.nandigrami.gmail.com> wrote:
> Dear AMBER Experts,
>
> I am facing an issue with running RNA simulations in AMBER. Attached is my
> input structure.
>
> Here is the error message:
>
> Error: an illegal memory access was encountered launching kernel
> kClearForces
> Error: an illegal memory access was encountered launching kernel
> kClearForces
> Error: operation not supported on global/shared address space launching
> kernel kClearForces
> Error: an illegal memory access was encountered launching kernel
> kClearForces
> Error: operation not supported on global/shared address space launching
> kernel kClearForces
>
> I also attached the md output log files. Any help would be much
> appreciated.
>
> Thank you very much.
>
> PN
>
>
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Received on Fri Jan 20 2023 - 13:00:06 PST
