Since nobody answered my question I will try to reformulate to make it
brief.
I am running an aMD (accelerated MD) according to the tutorial
http://ambermd.org/tutorials/advanced/tutorial22
The aMD step fails with cudaMemcpy error. I was able to overcome this
error by changing the ethreshp from -343484.5895 to -413484.5895 (that
is delta=-70000).
My QUESTIONS:
1. Do you thinks this simulation would still have a biological
significance after I`ve manually tuned this parameter?
2. Could this situation mean that my system is not properly relaxed
(although I`ve checked the density converges and RMSD plot goes flat)?
Thank you for your help.
Dmitry
On 08/12/2016 11:53 PM, Dmitry Suplatov wrote:
> Hello,
>
> I want to run aMD of a fairly large protein.
>
> The protein is a homo-4-mere, 1356 amino acids in total. The system -
> protein in TIP4PEW with ions according to 0.1M - contains 163 705 atoms.
>
> I implement the protocol according to the aMD tutorial
> (http://ambermd.org/tutorials/advanced/tutorial22):
> 1. Energy minimization in water with restraints on the protein (5000
> steps due to a large system)
> 2. Water shuffling with restraints on the protein (10 000 steps as in
> the original protocol)
> 3. Energy minimization with no restraints (10 000 steps due to a large
> system)
> 4. Heating in NVT from 0 to 300K in 250 000 steps with restraints on
> the protein (i`ve checked - no bubbles)
> 5. Equlibration in NPT - restraints are gradually removed in 12 steps
> (-0.25 kkal/molA2 per step), 85 ps per each step
> 6. Equilibration in NPT with no restraints - 10 ns (density converges)
> 7. Free dynamics in NVT for 1 ns
> 8. aMD
>
> The parameter file for aMD based on the freeMD is as follows:
> ----------------------------------------------------------------------------------
> Step-8: Accelerated MD in the NVT ensemble
> &cntrl
> imin=0, ! Flag to run minimization - No minimization
> irest=1, ! Flag to restart a simulation - Restart the
> simulation, reading coordinates and velocities from a previously saved
> restart file
> ntx=5, ! Option to read the initial coordinates,
> velocities and box size from the inpcrd file - Coordinates and
> velocities will be read
> nstlim=250000000, ! Number of MD-steps to be performed
> dt=0.002, ! The time step (psec). For temperatures above
> 300K, the step size should be reduced.
> ntc=2, ! Flag for SHAKE to perform bond length constraints
> - bonds involving hydrogen are constrained
> ntf=2, ! Force evaluation - bond interactions involving
> H-atoms omitted (use with ntc=2)
> cut=10, ! The nonbonded cutoff, in Angstroms
> ntb=1, ! Impose periodic boundaries at constant volume
> ntp=0, ! Flag for constant pressure dynamics - No pressure
> scaling
> ntt=3, ! Langevin thermostat
> gamma_ln=2.0, ! Collision frequency in ps−1 for Langevin thermostat
> ig=-1, ! Random seed for Langevin thermostat will be based
> on the current date and time
> temp0=300.0,! Reference temperature at which the system is to be kept,
> if ntt > 0.
> iwrap=1, ! The coordinates written to the restart and
> trajectory files will be wrapped into a primary box
> ntxo=2, ! Format of the final coordinates, velocities, and
> box size written to the restart file - NetCDF file
> ioutfm=1, ! The format of coordinate and velocity trajectory
> files - Binary NetCDF trajectory
> ntpr=10000, ! Print the progress of the run to output file every
> ntpr steps
> ntwr=10000, ! Every ntwr steps during dynamics, the “restrt”
> file will be written
> ntwx=10000, ! Every ntwx steps, the coordinates will be written
> to the mdcrd file
> iamd=3, ! Accelerated MD - boost the whole potential with
> an extra boost to the torsions
> ethreshd=22312.9234,
> alphad=1094.4,
> ethreshp=-343484.5895,
> alphap=26192.8,
> &end
> /
> ----------------------------------------------------------------------------------
>
> Launching the aMD with these parameters results in the following error:
>
> ----------------------------------------------------------------------------------
> cudaMemcpy GpuBuffer::Download failed an illegal memory access was
> encountered
> ----------------------------------------------------------------------------------
>
> The error is being reproduced on different hardware (GTX 980 Ti and
> Tesla K40s) and different units, while no error was previously
> observed on the same units with other Amber simulations, including aMD
> simulations of other proteins. Therefore I conclude that this is not a
> hardware issue.
>
> HERE I FINALLY COME TO THE POINT. Thank you for reading this far.
> When I "slightly" tune the ethreshp parameter and change it from
> -343484.5895 to -413484.5895 the simulation starts smoothly and
> continues to run.
>
> My QUESTIONS:
> 1. Do you thinks the resulting simulation would still have a
> biological significance after I`ve manually tuned this parameter?
> 2. Could this situation mean that my system is not properly relaxed
> (although I`ve checked the density converges and RMSD plot goes flat)?
>
> Thank you for your time.
> Best,
> Dmitry
>
>
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Received on Mon Aug 15 2016 - 04:00:02 PDT
