[gmx-users] Re: David, still confused with the alternating current
David van der Spoel
spoel at xray.bmc.uu.se
Mon Nov 22 11:30:56 CET 2004
On Mon, 2004-11-22 at 17:03 +0800, xieyh at hkusua.hku.hk wrote:
> 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?
I don't recall. So please try to reduce it from the source code...
> 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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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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