Hi,
I'm trying to run a simulation of a 12mer DNA
under 100 atm. In the beginning I tried to run it under constant pressure,
here's my input file.
12-mer DNA MD, 100atm
&cntrl
imin = 0, ntb = 0,
igb = 0, ntpr = 100, ntwx = 100,
ntt = 3, gamma_ln = 1.0,
tempi = 300.0, temp0 = 300.0
nstlim = 100000, dt = 0.001,
ntp = 0, pres0 = 100
cut = 12
/
However, the output file reported that the entire
simulation was performed at 0atm. I changed my input file to equilibrate the
pressure.
12-mer DNA MD , 12 angstrom cut off
&cntrl
imin = 0, ntb = 2,
igb = 0, ntpr = 250, ntwx = 250,
ntt = 3, gamma_ln = 1.0,
tempi = 300.0, temp0 = 300.0
nstlim = 100000, dt = 0.001,
ntp = 1, taup = 1.0, pres0 = 100,
cut = 12.0
/
The simulation ran for the entire weekend on a
quadcore 3GB processor.
Any insights would be very helpful.
Thanks
Sincerely
Yang Li
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Received on Mon Mar 22 2010 - 20:30:02 PDT
