On Mon, Aug 15, 2016 at 4:52 AM, DmitryASuplatov <genesup.gmail.com> wrote:
> 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?
Keep in mind that results from aMD only have "biological significance"
after they are re-weighted, and even then they are subject to the
usual caveats for MD simulations (requires close comparison to
experimental results etc etc). That said, all of the aMD parameters
are really "manual" parameters. There are some guidelines out there on
how to choose the alpha and threshold parameters, but if you deviate
it's not like you're wrong, and in fact you may get better results.
> 2. Could this situation mean that my system is not properly relaxed
> (although I`ve checked the density converges and RMSD plot goes flat)?
It could be a lot of things. Does the simulation always succeed if you
run with that new threshold, or conversely does it always fail with
the old threshold? Have you ensured your GPUs pass all the tests?
-Dan
>
> 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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--
-------------------------
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Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
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Received on Mon Aug 15 2016 - 11:30:02 PDT
