Hi,
To create the NMR restraints, I used the cpptraj rst function with masks
> :DUM.DU1 (for the dummy atom) and :WAT.O (for all water oxygens). In my
> dummy_rest.RST file I have:
>
> &rst iat=174099,-1,0
>
> r1=0, r2=0, r3=0, r4=50, rk2=0.000000, rk3=10.000000,
>
Someone else with more expertise can chime in, but from my experience that
feels like an incredibly large amount of restraints so I wouldn't be
surprised you have a slowdown. I'd try to trouble shoot it with runs
scaling the number of restraints, ie 17, 170, 1700 if you want a better
benchmark on what it's doing. It might also be worth considering weak
positional restraints on the oxygen of the water, given the volume you're
dealing with?
Best,
Kenneth
On Thu, Mar 16, 2023 at 1:10 PM Ava Waggett via AMBER <amber.ambermd.org>
wrote:
> Hello,
>
> I am simulating a water-octane interface. I am trying to use NMR restraints
> to maintain one virtual atom at the center of mass position for the water
> phase and another virtual atom at the center of mass of the octane phase.
>
> To create the NMR restraints, I used the cpptraj rst function with masks
> :DUM.DU1 (for the dummy atom) and :WAT.O (for all water oxygens). In my
> dummy_rest.RST file I have:
>
> &rst iat=174099,-1,0
>
> r1=0, r2=0, r3=0, r4=50, rk2=0.000000, rk3=10.000000,
>
>
> This is followed by the IG2(1) to IG2(3356) atom indices for the water
> oxygens. I have a similar distance restraint between the CoM of all octane
> C4's and my other virtual atom. I want the restraint to be centered at 0
> and was attempting to create a one-sided harmonic restraint.
>
>
> My system is ~170,000 atoms and when run on a NVIDIA 2080ti GPU, I can get
> ~150 ns/day with no restraints. However, when heating my system with these
> restraints, I am only getting *13 ns/day*.
>
>
> This is what my nvt.mdin file looks like:
>
>
> NVT Heating with HMR and distance restraints to virtual atoms
>
> &cntrl
>
> imin=0, ! 0=no minimization
>
> ntx=1, ! read coord with no initial vel
>
> irest=0, ! 0=do not restart
>
> nstlim=125000 ! number of MD steps; (0.5 ns)
>
> dt=0.004, ! timestep (ps)
>
> ntf=2, ! 2=omit H bond interactions
>
> ntc=2, ! 2=SHAKE. constrain H-bonds
>
> tempi=100.0, ! initial temperature (K)
>
> temp0=300, ! final temperature (K)
>
> ntpr=1000, ! print progress every x steps
>
> ntwx=1000, ! print coord every x steps
>
> ntwr=20000, ! print restrt every x steps
>
> ntb=1, ! 1=yes periodicity (constant volume)
>
> ntp=0, ! barostat; 0=no pressure scaling
>
> ntt=11, ! Bussi thermostat
>
> cut=8.0, ! non-bond cut off (A)
>
> nmropt=1, ! turn on restraints
>
> iwrap=1 ! wrap coordinates
>
> /
>
> &wt type='TEMP0', istep1=0, istep2=10000, value1=100.0, value2=300.0 /
>
> &wt type='TEMP0', istep1=10001, istep2=125000, value1=300.0, value2=300.0
> /
>
> &wt type='END' /
>
> DISANG=dummy_rest.RST
>
>
> I tried to remove the write out of the restraints and saw no improvement in
> speed. I also tried doubling the number of CPUs to check if these
> restraints were being handled on CPU rather than GPU - there was no change
> in performance when doubling CPUs. Is this significant slow down to be
> expected for this type of restraint, or is there a way to optimize this?
> Also, may I have set the restraints up incorrectly? Any help would be much
> appreciated!
>
>
> Thank you,
>
> Ava
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Received on Thu Mar 16 2023 - 11:00:03 PDT
