Dear Amber user/Authors,
I wanted to run my production MD with HMR. So, after preparing my
simulation, running minimization and equilibration steps, I used parmed
to change the H-mass.
{
parmed prmtop
HMassRepartition
outparm hmr.prmtop
}
After this I ran my production where I got the following error:
cudaMemcpy GpuBuffer::Download failed an illegal memory access was
encountered
This is my input file:
100ns MD
&cntrl
irest = 1, ! Restart calculation
ntx = 5, ! Positions and velocities read formatted
ntb=2, ! Constant Pressure
ntp = 1, ! Isotropic pressure scaling
taup = 5.0, ! Barostat relaxation time
ig = -1, ! Random seed for thermostat
cut = 10.0, ! Nonbonded cutoff in Angstroms
ntc = 2, ! SHAKE on for bonds with hydrogen
ntf = 2, ! No force evaluation for bonds with hydrogen
temp0 = 300.0, ! Simulation temperature (K)
ntt = 3, ! Langevin thermostat
gamma_ln = 5.0, ! Collision Frequency for thermostat
nstlim = 25000000, ! Number of MD steps
dt = 0.004, ! Timestep (ps)
ntpr = 100, ! Print to mdout every ntpr steps
ntwx = 1000, ! Write to trajectory file every ntwx steps
ntwr = 1000, ! Write a restart file every ntwr steps
ntxo=1, ! Write coordinate file in ASCII format
ioutfm=0, ! Write trajectory file in ASCII format
barostat=2, ! Berendsen
/
I tried running the simulation with the original topology file without HMR
& 2fs time step, and it runs perfectly fine.
Then, I tried running the simulation with HMR_topology & 2fs time step,
and it reported the same error.
Therefore I assumed there is a problem with the topology file.
The only warning I got while preparing topology file in Parmed is the
following:
AmberWarning: Molecule atoms are not contiguous! I am attempting to
reorder the atoms to fix this.
I tried loading the topology file and coordinate file in chimera, and i
got the following error:
fillCoordSet: coordinates [arg 2] must be 2-dimensional array
Can anyone help understand what's happening here and what should I do?
Thanks in Advance !
Aravind R
Junior Research Fellow
Ranabir Das lab
NCBS, GKVK
Bellary Road
Bengaluru 560065
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Received on Mon Sep 24 2018 - 04:00:02 PDT
