Re: amber-developers: Problem with SHAKE when icfe != 0

From: Ilyas Yildirim <>
Date: Sun, 19 Mar 2006 21:06:11 -0700

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):
HZ 1.008

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.


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
> > 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
> > did this is to see if SHAKE is constraining all of the H? type atoms.
> > it did not work.
> You should look at this carefully...Is the list of SHAKEN bonds
> on the two processors? Is there any bond that has a different
> bond length on the second thread than on the first? It would be good to
> 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
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