hi all
I am doing two calculations using the same structure with explicit and
implicit solvent for the same time length (5ns). Surprisingly, the implicit
calculation is actually twice longer than explicit simply because SHAKE is
on in explicit calculation thus time step is 2fs while in implicit
calculation it is 1fs. The simulation itself seems ok. But I'm worried that
I might miss something here. People generally say implicit calculations are
a lot faster.
Here are my inputs for the production run:
IMPLICIT:
&cntrl
imin = 0, ntb = 0,
igb = 5, ntpr = 5000, ntwx = 2500,
ntt = 3, gamma_ln = 1.0,
tempi = 300.0, temp0 = 300.0,
nstlim = 5000000, dt = 0.001,
cut = 12.0,
ntr=1,
ig=-1,
/
complex (>10)
8.0
RES 1
RES 15 16
RES 67 68
RES 78 79
RES 98 99
RES 109
END
END
EXPLICIT:
&cntrl
imin=0,irest=1,ntx=5,
nstlim=2500000,dt=0.002,
ntc=2,ntf=2,
cut=10.0, ntb=2, ntp=1, taup=1.0,
ntpr=5000, ntwx=2500,
ntt=3, gamma_ln=2.0,
ntr=1,
temp0=300.0, tempi=300.0, ig=-1
/
complex (>10)
8.0
RES 1
RES 15 16
RES 67 68
RES 78 79
RES 98 99
RES 109
END
END
Thanks for your input!
Victor
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Received on Wed Jan 18 2012 - 14:00:02 PST
