[AMBER] Error while creating topology file(HMassRepartition) in parmed

From: Aravind Ravichandran <raravind.ibab.ac.in>
Date: Mon, 24 Sep 2018 16:09:09 +0530

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
 outparm hmr.prmtop
After this I ran my production where I got the following error:

cudaMemcpy GpuBuffer::Download failed an illegal memory access was

This is my input file:

100ns MD
  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
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
Bellary Road
Bengaluru 560065

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Received on Mon Sep 24 2018 - 04:00:02 PDT
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