> Date: Fri, 24 Feb 2012 15:37:41 -0500
> From: case.biomaps.rutgers.edu
> To: amber.ambermd.org
> Subject: Re: [AMBER] Constant Temperature
>
> 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
>
>
Thanks Dac and Jason.
I'm using explicit ions in implicit solvent to explore ion dependency of structure, is this a good idea?
Or i must to do simulations with explicit solvent (because of explicit ions)?
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Received on Fri Feb 24 2012 - 13:00:03 PST
