[gmx-users] accleration group
David van der Spoel
spoel at xray.bmc.uu.se
Mon Jan 21 21:27:38 CET 2002
On Mon, 21 Jan 2002, Rui Qiao wrote:
> Thanks for the prompt response of Erik and David.
> So I guess what Gormacs do is to put a force on the system so that
>the net force is zero for the whole system, is this right?
> Actually I am trying to simulate flow in a channel (periodicity
>is removed in z-direction by some cut-off scheme), and I use the
>accleration as a way of making my fluid moving. On one hand, I freeze the
>wall atoms, and on the other hand, I give an accleration to all the fluid
>atoms. So there would be a center-of-mass velocity in my system and I put
> nstcomm = 100000000
Set this to 0 if you don't want c.o.m.m. removal
> in the .mdp file so that the velocity is not removed.
> The questions are:
> 1. Where does this correction actually applied on? Does it applies
>on wall atoms or fluid atoms? The latter case would be a tough thing for
Your system is composed of at least two groups, A and B, and each group
feels an acceleration. THe sum of the forces is zero
Sum_(i=1-N_A) m_i a_A + Sum_(i=1-N_B) m_i a_B = 0
In principle the force works on both wall and fluid atoms, but if you
freeze the wall, basically the force is zero.
> 2. If instead of freezing the wall, I constrait the wall atoms by
>some spring, then how the correction will be done for the wall atoms? In
>this case, the wall atoms will be pushed by the accleration, and this is
>not wanted in the simulation actually.
It is up to you what you think is realistic, i.e. what kind of wall you
have. If you want to simulate friction, then some mobility of the wall
would not be bad...
Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576, 75123 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://zorn.bmc.uu.se/~spoel
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