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 - 10:30:03 PDT
