AMBER Archive (2007)

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

From: David A. Case (case_at_scripps.edu)
Date: Sat May 19 2007 - 23:03:24 CDT

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

> Only atoms in the bases 19-26 were allowed to move by fitting
> restraints in the mme_init command.
>
> The typical input file goes as
> mm_options("cut=25.0, nsnb=100, gamma_ln=50, temp0=300, tempi=50,
> gb=1, kappa=0.19");
> mme_init(molMD, ":19-26:", "::ZZZ", dummy, NULL);
> md(3*molMD.natoms, 100000, xyz, f, v, mme);
> setmol_from_xyz(molMD, NULL, xyz);
> putpdb("test.pdb",molMD);
>
> >>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.

As I said, I have not tested the Langevin implementation for frozen atoms;
there could be something wrong there.

...dac

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