Hi, Gard
Are you using Amber18? The speed issue in using NFE has been fixed in
AMBER20,
the speed should be at least 60% of the regular MD even if you are running
a large system.
So you can upgrade to AMBER20 and retry, also please post some feedback
when you get the test
results, that would be great.
Best
Feng
On Wed, Jun 24, 2020 at 6:59 PM Gard Nelson <Gard.Nelson.immunitybio.com>
wrote:
> Thanks for the suggestion, Wesley. Unfortunately, it's still running slow
> with US too. I tried several difference CV types too with no luck.
>
> Do you happen to know which patches you have applied?
>
> Thanks,
> Gard
>
> On 6/23/20, 2:14 PM, "Wesley Michael Botello-Smith" <wmsmith.uci.edu>
> wrote:
>
> Interesting, I have run US using both INFE and NMROPT on pmemd.cuda and
> they seemed more or less comparable in speed... I haven't tried SMD
> with CV
> module though. My version of amber may be a few patches behind
> though...
> maybe something changed?
> Do you see the same slowdown with INFE US?
>
>
> On Mon, Jun 22, 2020 at 2:58 PM Gard Nelson <
> Gard.Nelson.immunitybio.com>
> wrote:
>
> > Hi all,
> >
> > I want to run some free energy calulations. I’ve used the NMRopt
> module
> > for simple distance-based restraints in the past, but some of the
> > collective variables and methods in the free energy module would be
> really
> > useful. I set up and ran a simple distance-based SMD calculation and
> found
> > that it slowed my simulation down ~10x (4.41 ns/day) compared to
> unbiased
> > MD (42.00 ns/day). I set up the same calculation (except US instead
> of SMD)
> > using nmropt instead and found the slowdown to be ~10% (37.53
> ns/day) which
> > is about what I’d expect. Additionally, the slowdown with nmropt is
> grows
> > with the number of atoms I include in the COM calculation, whereas
> with
> > SMD, the slowdown is constant whether I use 2 atoms or 700.
> >
> > Is this expected behavior or am I doing something wrong? I’m using
> > pmemd.cuda from amber18 with all the patches applied. I’ve pasted
> input
> > files for each simulation below. Let me know if you need any more
> info.
> >
> > Thanks for your help!
> > Gard
> >
> > SMD input
> > mdin:
> > NVT
> > &cntrl
> > imin=0,
> > irest=1,
> > ntx=5,
> > ntxo=2,
> > iwrap=1,
> > ioutfm=1,
> > ntb=1,
> > ntp=0,
> > cut=8.0,
> > nstlim=5000000,
> > dt=0.002,
> > ntf=2,
> > ntc=2,
> > temp0=300.0,
> > ntpr=5000,
> > ntwx=50000,
> > ntt=3,
> > gamma_ln=5.0,
> > ig=-1,
> > infe=1,
> > /
> > &ewald
> > /
> > &smd
> > output_file = 'smd.dat'
> > output_freq = 5000
> > cv_file = 'def_CV-SMD'
> > /
> >
> > cv_file:
> > &colvar
> > cv_type = 'DISTANCE'
> > cv_ni = 2
> > cv_i = 5119,13218
> > npath = 2
> > path = 0.0,100.0
> > path_mode = 'LINES'
> > nharm = 1
> > harm = 0.0
> > /
> >
> >
> > US input
> > mdin:
> > NVT
> > &cntrl
> > imin=0,
> > irest=1,
> > ntx=5,
> > ntxo=2,
> > iwrap=1,
> > ioutfm=1,
> > ntb=1,
> > ntp=0,
> > cut=8.0,
> > nstlim=50000,
> > dt=0.002,
> > ntf=2,
> > ntc=2,
> > temp0=300.0,
> > ntpr=5000,
> > ntwx=5000,
> > ntt=3,
> > gamma_ln=5.0,
> > ig=-1,
> > nmropt=1
> > /
> > &ewald
> > /
> > &wt
> > type='DUMPFREQ'
> > istep1=5000
> > /
> > &wt
> > type='END'
> > /
> > DISANG=d-rst
> > DUMPAVE=01_NVT.US.dat
> >
> > DISANG:
> > US window
> > &rst
> > iat=-1,-1,
> > igr1=5119,5259,
> > igr2=13218,13371,
> > r1=40,
> > r2=50,
> > r3=50,
> > r4=60,
> > rk2=0,
> > rk3=0,
> > fxyz=1,1,1,
> > outxyz=1
> > /
> >
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--
Feng Pan
PostDoc
Florida State University
Department of Statistics
Email: fpan3.ncsu.edu; fpan.fsu.edu
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Received on Thu Jul 09 2020 - 22:30:03 PDT
