From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Thu Jan 22 2004 - 17:19:22 CST
Hi,
The coupling constants have units of 1/ps, so you would put 2.5 in the B
column of the PDB file. Here's a snip of the relevant source code:
void Sequencer::tcoupleVelocities(BigReal dt_fs, int step)
{
if ( simParams->tCoupleOn )
{
FullAtom *a = patch->atom.begin();
int numAtoms = patch->numAtoms;
BigReal coefficient = broadcast->tcoupleCoefficient.get(step);
Molecule *molecule = Node::Object()->molecule;
BigReal dt = dt_fs * 0.001; // convert to ps
coefficient *= dt;
for ( int i = 0; i < numAtoms; ++i )
{
int aid = a[i].id;
BigReal f1 = exp( coefficient * molecule->langevin_param(aid) );
a[i].velocity *= f1;
}
}
}
This is a pretty old method. I'd suggest using Langevin personally.
-Jim
On Tue, 20 Jan 2004, Hyonseok Hwang wrote:
> Dear All,
>
> I would like to use the 'Berendsen's temperature coupling method' in
> NAMD. In that method, a coupling constant of 0.4ps is generally
> recommended. Then my question is what value I should put in the B
> column, which is now designated as the 'tCouplecol'. Do I should put 0.4?
>
> Thank you very much.
>
> -Hyonseok Hwang
>
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