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
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Received on Mon Sep 17 2012 - 14:00:02 PDT
