Daniel, thank you for your response.
I intend to use aMD to obtain a more complete sampling of my protein. I
will then select particular conformations for docking. I believe I do
not need re-weighting for this.
Please comment.
Thank you for your time.
Dmitry
On 08/15/2016 10:00 PM, amber-request.ambermd.org wrote:
> 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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Received on Tue Aug 16 2016 - 04:30:02 PDT
