If all you want are conformations that seems fine.
-Dan
On Tue, Aug 16, 2016 at 5:05 AM, DmitryASuplatov <genesup.gmail.com> wrote:
> 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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>>> >AMBER.ambermd.org
>>> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
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--
-------------------------
Daniel R. Roe, PhD
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
(801) 585-6208 (Fax)
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Received on Tue Aug 16 2016 - 08:00:07 PDT
