I have changed the dummy atom type from DH to HA, H and HZ (also HD). For
HA and H, both threads gave the same results. For HZ and HD, it gave
different results, and the system blows up at the end. I use the same
extra.frcmod file (except changing the atom type). Here is the .frcmod
file I am using (the first parts which has the bond info.s in it):
-----------------------------------------------------
MASS
HZ 1.008
BOND
O -HZ 434.0 1.010 [N2-H]
CA-N* 424.0 1.383 [C-N*]
.
.
.
-----------------------------------------------------
Originally, it was
O -DH 434.0 1.010 [N2-H]
I have changed this atom type to H, HA, HZ, and HD.
I think that SHAKE is turning on the SHAKE constraints of specific
hydrogen types, not all H-types. I would like to know if this is true.
Best,
On Sat, 18 Mar 2006, David A. Case wrote:
> On Sat, Mar 18, 2006, Ilyas Yildirim wrote:
> >
> > I have done something else, too, but that did not work. I changed all
of
> > the DH type to HZ type (which is defined in the parm.99 too). In the
> > frcmod file, I entered the dummy atom parameters to HZ. The reason why
I
> > did this is to see if SHAKE is constraining all of the H? type atoms.
And
> > it did not work.
>
> You should look at this carefully...Is the list of SHAKEN bonds
different
> on the two processors? Is there any bond that has a different
equilibrium
> bond length on the second thread than on the first? It would be good to
track
> down what is going on here, so that we can add more checks in the code.
>
> ...thanks!...dave
>
>
--
Ilyas Yildirim
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Received on Wed Apr 05 2006 - 23:49:36 PDT
