Please see: http://archive.ambermd.org/201808/0273.html
Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)
Web: http://www.agarwal-lab.org/
On 5/8/2019 11:50 AM, Akshay Prabhakant wrote:
Please find below, the links to my simulation input files:
1.
https://pastebin.com/raw/xfLVbHMq : 100ps equilibration at 300K
2.
https://pastebin.com/raw/PCC7Eq4Y : COM_dist.RST = the
restraint file used in the aforementioned simulation
Minimization and NVT equilibration have already run successfully using
pmemd.cuda
When I run the above simulation using pmemd.MPI, it runs successfully, the
command used was:
mpirun pmemd.MPI -O -i npt_02.in -o npt_02.cpu.out -p apo_cap.prmtop -r
npt_02.cpu.rst -c npt_01.rst -inf npt_02.cpu.mdinfo
The command used, while running the simulaiton on pmemd.cuda:
pmemd.cuda -O -i npt_02.in -o npt_02.cpu.out -p apo_cap.prmtop -r
npt_02.cpu.rst -c npt_01.rst -inf npt_02.cpu.mdinfo
However, when i run it using omemd.cuda, it throws the error: "cudaMemcpy
GpuBuffer::Download failed an illegal memory access was encountered", but
sometimes it might also throw
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.
Can you help me understand why it runs on pmemd.MPI and what I can do to
make it run on pmemd.cuda ?
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Received on Wed May 08 2019 - 09:30:02 PDT
