The distance between the Zn and the O in the water molecule is
consistent throughout the entire simulation. Though it is a bit closer
than I would expect it to be, it stands around 1.8 A in average (the
reference value in the frcmod file is 2.2 A).
Fabrício
2012/9/17 M. L. Dodson <mldodson.comcast.net>:
> 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
>>
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>
> --
> 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
>
>
>
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Received on Mon Sep 17 2012 - 15:00:03 PDT
