From: Jérôme Hénin (jhenin_at_ifr88.cnrs-mrs.fr)
Date: Wed May 12 2010 - 02:31:51 CDT
If there are many molecules of type A and B, then TclBC is probably
the most efficient way. If there are few of them, you could define the
restraints with the "Collective Variables" module, using the distanceZ
and distanceXY components. You can either use relative restraints
between two groups, or create absolute restraints by including "dummy
atoms", which are just a preset, fixed position (see the dummyAtom
keyword in the user's guide).
On 11 May 2010 22:45, Eduardo Cruz-Chu <chucruz_at_ks.uiuc.edu> wrote:
> there is a way; but for such special cases, there are no NAMD commands. You
> must write the procedure/method using tcl commands.
> you may want to take a look at the user-defined force tutorial at:
> On Tue, 11 May 2010, muniyamuthu.raviprasad_at_ndsu.edu wrote:
>> I have a molecular model with two different types of molecules ( say A and
>> I want to set the constraints to molecule-A like this : Free in Z -
>> direction and fixed in X , Y direction. This can be done under constraint
>> setup.I am OK with that. but in the same model,
>> I want set the constraints to molecule-B like this: Free movement in X , Y
>> direction. Free movement in Z direction but between Z = -2 to Z= +2.
>> Is there any way to set up this kind of constraints?
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