Re: [AMBER] MD simulation parameters: urgent please

From: David A Case <>
Date: Mon, 1 Jul 2013 21:38:11 -0400

On Mon, Jul 01, 2013, Mary Varughese wrote:
> in the production dynamics(in NPT):
> when ntb=2, ntp=1, pres0=1.0, ntt=3
> 1: what should be the appropriate value of gamma_ln ? (i have used 1 )
> does increasing value to 5.0 has any advantage

I doubt that you could see any difference between 1 and 5.

> 2: also what is the significance of taup=2.0 ; how does it affect the
> dynamics

The affects the speed at which the volume of the system responds to pressure
fluctuations, and hence to the magnitude of the fluctuations themselves.
If your system is too small (doesn't have enough water molecules) the value
of this variable might cause a noticeable difference, although I have not
personally seen such a case.

> 3: also should i essentiallly include ig=-1 as it says in amber DNA
> tutorials in the case of ntt=3.

Yes: this is essential.

> 4: Also i hope adding these values doesnt affect mmpbsa calculations.

Not setting ig=-1 could lead to very bad results. Minor variations in
gamma_ln or taup are unlikely to have measurable effets.

> 5: Also sir does iwrap=1 has any influence on mmpbsa calculations?

It can. The safest course of action is to use the "autoimage" command in
cpptraj before handing things off to mm-pbsa. Also, be sure to visualize
your trajectory (after autoimage) to make sure there are no wrapping


p.s.: be sure to study reviews of mm-pbsa calculations, and look for
papers that report calculations similar to the ones you are planning. In
my opinion, a careful study of what happens during your simulation is a
lot more likely to lead to new insights than are the energies that come
out of the mmpbsa analysis.

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Received on Mon Jul 01 2013 - 19:00:02 PDT
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