DANIELE at biop.ox.ac.uk
Sat Jun 7 16:59:33 CEST 2003
Thanks for this, things begin to be clearer. Now, what is the criterion
according to which, for instance, "f_i" must be added to the virial in
box "t1", "f_j" to the "CENTRAL" box, "f_k" to "t2", and so on ? I
mean, how are the values of "t1", "t2" and "t3" chosen ? If the
answer is in appendix B (single sum virial), then I suppose I need to
understand what "[...] pick one of the grey atoms (atom j) and give it
the correct periodicity w.r.t. any of its black neighbours [...]" means.
Is it correct if I say that it means "pick atom j and consider the
distance of its nearest image from i" ? So, assuming the central box is
number 13, why sometimes do I get either "t1" or "t2" or "t3" different
from 13 even when in the last line of my .gro file I set the box
dimensions ~200 times larger than x_minimum, x_maximus, y_minimum,
y_maximus, z_minimum, z_maximus of my molecule, thus expecting the
nearest distance always being in the central box ?
On 6 Jun 2003, David wrote:
> On Fri, 2003-06-06 at 20:30, Daniele Bemporad wrote:
> > Hi all, hi David
> > In the previous e-mail I forgot to also ask about "fshift[is3]" in
> > innerc.c and its arguments is3, is3+1, is3+2.
> > The problem is that if I change the calculation of the force and I update
> > the variable "f [atom number] [x, y or z axis]" , I get NO effect on the
> > atomic positions, unless I also update this (still mysterious to me)
> > variable "fshift". What is this about ? Can please anybody tell me what
> > exactly the 2 elements of the array are in bonded and non-bonded
> > interactions: fr->fshift[1st_element][2nd_element] ?
> This is the total force exerted on each of the 27 copies of the unit
> cell. This force is only used for computing the virial.
> It is an array of 27 vectors with X,Y,Z component.
> If your modification has no effect, then you may be using another
> routine than you think you are (there are > 70 different innerloop
> routines). Bonded forces are somewhat more straightforward.
> > Thanks a lot
> > Daniele Bemporad
> > On 6 Jun 2003, David wrote:
> > > On Fri, 2003-06-06 at 19:47, Daniele Bemporad wrote:
> > > > Hi all
> > > > Can anybody please explain me or tell me where I can find an explanation
> > > > for the variable "fr->fshift[*]" (with *=t1,t2,t3,CENTRAL) in subroutines
> > > > "do_dih_fup" and "angles" in file bondfree.c ? And an explanation for its
> > > > arguments t1,t2,t3,CENTRAL ?
> > > there's a bit of an explanation in the appendix of the manual.
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