spoel at xray.bmc.uu.se
Fri Jun 6 17:28:33 CEST 2003
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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Dr. David van der Spoel, Dept. of Cell and Molecular Biology
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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