Hi David and Bill,
Sorry for the delay in my response. I wanted to play with the simulation
and try a few things. 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. DAvid i tried to turn
off shake off and FAIL, I get this error: "ANDER BOMB in subroutine
nonbond_list
volume of ucell too big, too many subcells
list grid memory needs to be reallocated, restart sander"
So.... I tried increasing the water buffer from 12 to 50A and I recieve
this error, " Cutoff list exceeds largest sphere in unit cell!!
Big problems with imaging!!
a,b,c = -121.341151445557 -121.341151445557
-121.341151445557
alpha,beta,gamma = 90.0000000000000 90.0000000000000
90.0000000000000
cutlist,sphere = 14.0000000000000 -182.011727168336"
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. I hope you guys have some ideas
or can help me see the problem.
thanks thanks thanks!!
-justine
On Thu, Sep 23, 2010 at 3:02 PM, case <case.biomaps.rutgers.edu> wrote:
> On Thu, Sep 23, 2010, Justine Shaw wrote:
>
> > Hope you can help me solve a tiny problem I am having with a simulation.
> I
> > am simulating a bis(N-methylimidazole)- meso-tetraphenyl iron porphyrin
> in
> > water. I keep getting shake errors even when i heat the structure
> slowly
> > using NMR constraints.
>
> There is likely to be something odd about the force field. Can you
> minimize
> the structure OK without shake? Does MD work ok without shake? What time
> step are you using?
>
> I think the shake error message tells you which bond had the problem. Can
> you look at the structure in that part of the molecule to see if there is
> anything funny going on?
>
> ...good luck...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
*****************************
Justine A. Shaw -PhD Candidate
ΦΛΥ '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 Mon Oct 11 2010 - 13:00:04 PDT
