Re: [AMBER] Error in umbrella sampling

From: Saikat Pal <>
Date: Tue, 18 Sep 2018 14:30:02 +0000 (UTC)

In GPU I am getting the following error:

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.

cudaMemcpy GpuBuffer::Download failed an illegal memory access was encountered

Thanks and Regards,
Saikat Pal


    On Monday, 17 September, 2018, 10:53:41 PM IST, Saikat Pal <> wrote:
 In cpu :
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0x14B357B2DE08
#1  0x14B357B2CF90
#2  0x14B35725E4AF
#3  0x46B177 in __pme_slab_recip_mod_MOD_do_slab_pmesh_kspace
#4  0x47D507 in __pme_force_mod_MOD_pme_force
#5  0x4A4BBC in __runmin_mod_MOD_runmin_master
#6  0x4C76E2 in MAIN__ at pmemd.F90:?

In gpu :
At line 137 of file inpcrd_dat.F90 (unit = 9, file = 'equil_4_5.rst')
Fortran runtime error: End of file

Thanks and Regards,
Saikat Pal


    On Monday, 17 September, 2018, 10:40:49 PM IST, David A Case <> wrote:
 On Mon, Sep 17, 2018, Saikat Pal wrote:

> When I have performed umbrella sampling using center of mass in cpu
> using  following script  :


> It works fine.But its not working in gpu.

Can you say what the error is?  (That's often quite informative, and
might relieve people on the list from having to try to reproduce the
problem, given only a small piece of the mdin file.)

> It works fine in gpu but not working in cpu.

Same question as above.


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