Hey Bill,
Thanks for the reply. 1.33 angstroms was not a typo, I’m saying that the N-H bond length is initially the correct value of 1.01 angstrom when SHAKE is used with MM on a GPU cluster and later the bond elongates to 1.33 angstroms after switching to using QM/MM on a CPU cluster. However, if I turn shake off when performing QM/MM the N-H bond will oscillate around the equilibrate value of 1.01 angstroms.
The fact that the bond length is correct initially and will also oscillate around the correct value leads me to believe the problem isn’t in my parameters.
Best,
Jon
> On Dec 28, 2020, at 10:08 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> Initially it was 1.01 with shake, then later 1.33 when shake was turned
> back on? If the second was a typo and 1.01 is with shake consistently,
> that implies the atom has an 'H' in its type (I think), but the actual
> type might be non-H, maybe through atom type aliasing(?) or the
> type-type potential is wrong. Job 1 is check the types and look up what
> equilibrium distance is defined.
>
> How are you measuring? I wonder if you're measuring the same bond
> consistently? 1.33 would be a C-C double bond.
>
> I've never used QM/MM.
>
> Bill
>
> On 12/27/20 9:26 PM, Jonathan Church wrote:
>> Hello,
>>
>> I ran into a problem using the SHAKE algorithm and I was curious if anyone had seen anything similar. I have a protein with a ligand attached embedded in a lipid bilayer. I equilibrated this system classically for about 300ns using GPU’s with CUDA from AMBER16 and during that time I used SHAKE.
>>
>> After about 300ns I then switched to using QM/MM with DFTB2+D and sander MPI. After I switched to using QM/MM with SHAKE, an N-H bond of the peptide backbone of an ILE residue about 15 angstroms from the QM region elongates to 1.33 angstrom when it was 1.01 angstrom for the entire MM equilibration period. If I turn SHAKE off the peptide N-H bond will oscillate around the 1.01 angstrom value. However as soon as I turn SHAKE back on, the bond elongates back to 1.33 angstrom.
>>
>> Has anyone else seen anything like this?
>>
>> Best,
>> Jon
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Received on Tue Dec 29 2020 - 09:00:02 PST
