[gmx-users] Re: David, still confused with the alternating current

xieyh at hkusua.hku.hk xieyh at hkusua.hku.hk
Mon Nov 22 10:03:35 CET 2004

Dear David:
Thanks for your kind reply. 
But, to my question, the key point is what the mdp options should be for
oscillating field, and what is the input format for alternating current. 

For instance, to the direct current electric field, the option ¡§E_z = 1   0.2 
0.0¡¨ should be added to *.mdp file before ¡¥mdrun¡¦. 

So correspondingly, what should we do to E_zt under alternating current case?
Thanks very much.
Xie YH
The Univ. of Hong Kong
On Mon, 2004-11-22 at 03:54 +0800, xieyh at hkusua.hku.hk wrote:
> Dear David:
> As you suggested, I have downloaded and installed the GMX CVS version for the
> applying of alternating current (AC) electric field (EF).However, my purpose
> can not yet be realized. Maybe, you can give me much more help.
> Compared with GMX3.1 version, the source code about the electric field has
> modified as shown in /src/mdlib/sim_util.c, also listed in the following. 
> I think this part of code is fully considering the alternating current
> field. Howerver, I made some tries, then the AC electric field could not be
> applied. In other words, although the source code is modified, what is mdp
> options about AC electric field? As known, for direct current (DC) electric
> field: "E_z = 1.0   0.2   0.0" denotes an electric field with frequency=0 and
> strength=0.2. 
> If applying the time-dependent AC electric field, some items need to be added
> into E_zt options. So can you give me a light about what is the E_zt option?
> For example, I want to apply a AC electric field: E = E0*cos (omega*t + phi),
> what is the corresponding definition in E_zt option?
You need to supply either a static and an oscillating field. Please try
to deduce from the source code which values are reasonable. Note that
the input is in V/nm, and that you can print the resulting field with a
command line option to mdrun.

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