On Fri, Feb 24, 2012, amir abbasi wrote:
>
> I'm trying to simulate a small nucleic acid molecule (5 nt) in implicit
> solvent and constant temperature (300 K).
> But i got a broad range of temperature from 250 K to 350 K.
> This is my MD input file:
> &cntrl
> imin = 0,
> ntb = 0,igb=1,
> ntt = 3, gamma_ln = 1.0,
> tempi = 300, temp0 = 300,
> nstlim = 100000000, dt = 0.001,
> ntpr = 100, ntwx = 100, ntwr = 1000
> cut = 12.0
> /
See Jason's response, which is a good one. But you could also increase
gamma_ln to a bigger value: 5 is often used for conformational exploration,
and values on the order of 50 correspond to the viscosity of water. It kind
of depends on what you want to learn from the simulation.
....good luck...dac
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Received on Fri Feb 24 2012 - 13:00:02 PST
