Victor,
You may want to look at the methodology for the INTERFACE force field for simulating metal and metal oxide surfaces (
https://pubs.acs.org/doi/10.1021/acs.jctc.3c00750). I don’t know if INTERFACE already has parameters for ZrO2, but maybe you can draw inspiration to develop your own. (There is also a tutorial using INTERFACE with AMBER:
https://ambermd.org/tutorials/advanced/tutorial27/index.php)
I, too, once wanted to study the interaction of a biopolymer with a surface, so I’ll add that complexity doesn’t stop with obtaining the parameters to run the simulation. As always with MD, you really need to consider if the phenomenon of interest occurs on a timescale you can reasonably simulate. Also, how are you going to select the initial orientation(s) of the biopolymer with respect to the surface? These (and other) issues have been encountered before in the lit. (for cytochrome c on Au, for example); I just mention them to raise awareness of the challenges beyond getting even somewhat reasonable force field parameters.
Hope this was helpful!
Best,
Matthew
> On Jan 10, 2024, at 2:24 PM, Victor Nazarychev via AMBER <amber.ambermd.org> wrote:
>
> *Message sent from a system outside of UConn.*
>
>
> Hello Thomas,
>
> Thank you for your response. Previously, for TiO2, I found a paper
> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpubs.acs.org%2Fdoi%2Ffull%2F10.1021%2Facs.jpcc.5b02669&data=05%7C02%7Cmatthew.guberman-pfeffer%40uconn.edu%7Cfa24065bb22a40d1303a08dc1211d6c4%7C17f1a87e2a254eaab9df9d439034b080%7C0%7C0%7C638405115024788254%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ESsnMtozx2N7LpLOmqOTP2czJtPU8YnRKGv%2BeNrkOyU%3D&reserved=0 in which the VDW
> and partial charges for Ti and O atom types were shown that could be used
> with the Amber force field.
>
> As like for TiO2, someone may have previously obtained the VDW parameters
> and partial charges for ZrO2. I preliminarily understand how to build the
> topology and coordinate files for ZrO2. However, it is not clear how to
> calculate the VDW parameters for Zr and O atom types in ZrO2 that might be
> used with GAFF. If possible, someone might suggest a way to calculate these
> VDW parameters or a previous study in which these parameters were evaluated.
>
>
> Best regards,
>
> Victor
>
> ср, 10 янв. 2024 г. в 18:28, Steinbrecher, Thomas <
> thomas.steinbrecher.roche.com <mailto:thomas.steinbrecher.roche.com>>:
>
>> Hi Victor,
>>
>> possible to simulate yes, but I am quite certain no useable parameters
>> will be available, you would have to build your own ZrO2 model and that
>> sounds like a difficult thing to get right in molecular dynamics.
>>
>> Kind Regards,
>>
>> Thomas
>>
>> On Wed, Jan 10, 2024 at 4:06 PM Victor Nazarychev via AMBER <
>> amber.ambermd.org <mailto:amber.ambermd.org>> wrote:
>>
>>> **Warning** The sender address (Victor Nazarychev via AMBER ) can not be
>>> verified, sender email address could be spoofed. Please take care to
>>> proceed.
>>> Dear Amber's users,
>>>
>>> Is it possible to simulate the interaction of the biopolymers
>>> parametrized
>>> in the GAFF force field with the surface of ZrO2?
>>>
>>> Maybe some parametrization of the VDW of partial charge interactions for
>>> ZrO2 exists for the Amber force field family?
>>>
>>>
>>> Best regards,
>>>
>>> Victor
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>>>
>>>
>>
>> --
>> *Dr. Thomas Steinbrecher*
>> Principal Scientist CADD
>>
>> Roche Pharma Research and Early Development
>> Roche Innovation Center Basel
>> F. Hoffmann-La Roche Ltd
>> Bldg. 092/3.92
>> Grenzacherstrasse 124
>> 4070 Basel
>> Switzerland
>>
>> Phone +41 61 682 1319
>> mailto: thomas.steinbrecher.roche.com <mailto:thomas.steinbrecher.roche.com>
>>
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Received on Wed Jan 10 2024 - 13:00:02 PST
