AMBER Archive (2007)

Subject: Re: AMBER: Temperature Drift in MD (NAB)

From: David A. Case (case_at_scripps.edu)
Date: Fri May 18 2007 - 18:07:09 CDT

On Fri, May 18, 2007, adelene_at_stanford.edu wrote:

> Hi, in my MD simulation (freezing 1141 atoms, moving 255) using NAB
> and options shown below, the temperature drifts from the set 300K to
> an average of 290.5K.

What do you mean by "freezing"? (ibelly?) It is certainly possible that the
Langevin implementation has a bias with frozen atoms: I haven't tested this
myself.

>
> I'm not sure if this is a problem due to the coupling parameters I've
> chosen, and would appreciate some advice on this. Should I be using
> the Berendsen coupling, or is Langevin a better option given an
> implicit GB run?
>
> MD options:
> cut=25;
> gamma_ln=50;
> tempi=50;
> gb=1;
> kappa=0.19;

Above look fine to me....How about dt, and so on? Can't you give the complete
input file?

....dac

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