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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Received on Mon Jun 22 2020 - 15:00:03 PDT
