This may be wildly off base, but is the water still at a distance from
the Zn consistent with the distance you found when you parameterized
the system? What I am getting at is: has the Zn-associated water diffused
away? What is the distance in the last restart file before the simulation
stopped compared to the parameterized distance?
Bud Dodson
On Sep 17, 2012, at 3:46 PM, Fabrício Bracht wrote:
> Hello. I have already had long discussions regarding this system in
> specific (http://archive.ambermd.org/201208/0174.html). The last
> discussion ended with my email:
>> I have deleted the bonds between the hydrogen atoms for this
>> particular water molecule (bound to the zinc atom). Used the flexible
>> water model and now the angle parameter for this water molecule is in
>> use. The md simulation has worked and the problem seems to be solved.
>> Are there any extra advices or perhaps some reading material I could
>> use to better understand the difference between using the flexible
>> water model or not?
>> Thank you again
>> Best regards
>> Fabrício
> I have not found the link for this particular discussion yet. The
> system is composed of an enzime with a zinc atom in its catalytic
> site. I have successfully run several hundred ns for a very very
> sismilar system, in which bound to the zinc atom is a hydroxyl group.
> This system now has a water molecule bound to the zinc atom. In my
> last discussion I have found that the only way for me to continue
> using the angle force parameters for this particular water molecule
> (which were the parameters that the MTK++ procedure gave), was to turn
> the flexible water model on. Now, the system has no apparent
> structural problems (bad geometry or collapsing hydrogen atoms etc),
> and yet, I still get the following error when I try to run pmemd.cuda.
>
> cudaMemcpy GpuBuffer::Download failed unspecified launch failure
>
> The error does not stop, however, the simulation from being restarted
> from the point where it has ended. I am running right now the same
> simulation under sander.MPI. But the system is quite large and I do
> not expect the results are in until the end of this week. By changing
> the seed I can, sometimes, run the entire simulation without any error
> messages. But then again, sometimes, it only takes a few steps for the
> simulation to stop. In previous discussions, I have discovered that
> the error is precision model independent (using either SPFP or SPDP or
> DPDP). The parameters for the similar system with the hydroxyl ion are
> very similar to this one, except for some specific bond constants
> (like the ZN-HOH bond and the H --- O bond) and, of course, the
> charge distribution. But other than that, the two systems are very
> alike.
> Any help here would be appreciated
> Fabrício
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
M. L. Dodson
Business email: activesitedynamics-at-gmail-dot-com
Personal email: mldodson-at-comcast-dot-net
Gmail: mlesterdodson-at-gmail-dot-com
Phone: eight_three_two-five_63-386_one
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Sep 17 2012 - 14:30:03 PDT
