Now I am getting seg fault errors running with no shake and an NTP
simulation!?
On Mon, Oct 11, 2010 at 3:07 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > I watched the movies Bill and i cant find anything
> > "strange" goign on. Maybe its something funky with the hydrogens on the
> > waters which are hard to see with so many of them.
>
> You may have to go back and save each step to mdcrd to see anything
> happening. Additionally, did you look at the specific atoms
> mentioned in the shake failure output?
>
> > ...
> > So then....... I try going back to 12A buffer no shake and setting Taup =
> > 20.0 as I read in another thread in our newsgroup. When I do that the
> > simulation stops at about 300 ish psec. I check the output and the
> pressure
> > fluctuates wildly with an NPT simulation.
>
> Wild fluctuation is normal for NPT. No shake is not really
> appropriate for simulations with TIP3 water, because the water
> model depends on shake to keep the vdw-free H within the O radius
> (minimization will sometimes be ok).
>
> Bill
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*****************************
Justine A. Shaw -PhD Candidate
ÖËÕ '09-'10 Service Chair
Profs. Ratner and Meade Research Groups
Department of Chemistry
Northwestern University
Office: 4039 Nano (Ryan Hall)
Office Phone: 847 467 4991
Cell: 773-354-7135
Email: j-shaw.northwestern.edu
*************************************
"Let's do this....!"
-Justine Shaw
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 12 2010 - 11:30:03 PDT
