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

From: Ilyas Yildirim <>
Date: Sat, 18 Mar 2006 00:26:02 -0700

Dear Dave,

I have followed your suggestion, and after 10 ps, I dont see anything
strange happening. Namely, everything works fine. The file I use is
the following:

-------------------------- ---------------------------------------
    100000 fs simulation
      noshakemask = '.%DH | (.%H & !.H1)',
Here, $lambda = 0.5 (in the test I have been doing). It works with icfe=1.

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. I dont know why this happened. Anyways, noshakemask is a
very nice solution. Thanks.


On Fri, 17 Mar 2006, David A. Case wrote:

> On Thu, Mar 16, 2006, Ilyas Yildirim wrote:
> >
> > 4. When SHAKE is turned on (see ./ntc_2_ntf_2_icfe_1_ntb_1), the
> > blows up.
> Have you read note (5) on p. 156 of the Users' Manual. Amber right now
> a check that the *number* of shaken bonds is the same in both states,
but it
> does not really check that the list of shaken bonds is identical (with
> identical equilibrium bond lengths.) Patches to further validate the
> files would be welcome.
> >
> > The reason why it does not work when SHAKE is turned ON is because of
> > DH bonds. I think SHAKE is just constraining the H-bonds, not
> > DH-bonds are also like H-bonds, but the atom type for these dummy
> > are DH, not H or H?.
> It uses the element type in LEaP (I think). So you would have to tell
> that your dummy atoms are hydrogens. But using noshakemask would be a
> solution. It would be great if you could try this (add noshakemask,
> ntc=2) since it has not been tested very much.
> ...thanks!...dave

  Ilyas Yildirim
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  -			-
Received on Wed Apr 05 2006 - 23:49:37 PDT
Custom Search