Hi,
If I need to change two reaction coordinates simultaneously(or even more),
how should I do or where should I start? Is there any instructions to do
so? Thanks!
Best,
Jing
Jing Qu <jqu2.ncsu.edu>于2023年9月8日 周五19:19写道：
> Yes it's more like that. Thank you. I'll have a look at it and have a try.
>
> Carlos Simmerling <carlos.simmerling.gmail.com>于2023年9月8日 周五18:09写道：
>
>> Do you mean the base rotates out of the duplex? In that case maybe look
>> at this article
>>
>> An Improved Reaction Coordinate for Nucleic Acid Base Flipping Studies
>> https://doi.org/10.1021/ct9001575
>>
>>
>> On Fri, Sep 8, 2023, 5:15 PM Jing Qu <jqu2.ncsu.edu> wrote:
>>
>>> Hi,
>>>
>>> If you're referring to variations of chi torsion angles then that's not
>>> what I'm trying to say here. I mean that the bases rotate around the z-axis
>>> (which is the normal vector to the base plane) with the C1' atom as the
>>> origin. Or with the other end of the glycosidic bond as the origin. Or
>>> maybe even rotating the base and the sugar ring together as a whole.
>>>
>>> Best,
>>> Jing
>>>
>>> On Fri, Sep 8, 2023 at 4:58 PM Carlos Simmerling <
>>> carlos.simmerling.gmail.com> wrote:
>>>
>>>> If you mean rotation of the base around the glycosidic angle, you can
>>>> use a dihedral restraint.
>>>> This old reference might help
>>>> https://doi.org/10.1021/ja075128w
>>>>
>>>> On Fri, Sep 8, 2023, 4:52 PM Jing Qu via AMBER <amber.ambermd.org>
>>>> wrote:
>>>>
>>>>> Dear all,
>>>>>
>>>>> I am learning to perform the Umbrella Sampling to get the PMF between
>>>>> two
>>>>> states of a DNA strand. And I have trouble determining the reaction
>>>>> coordinates. The difference between the two states is that the hydrogen
>>>>> bonds they form are not the same. I think the transition is more like
>>>>> rotating the base in the plane of the base ring (around the z-axis). I
>>>>> see
>>>>> that the tutorial examples on Amber's site use reaction coordinates
>>>>> like
>>>>> angles or distances. But I can't think of any angle that would control
>>>>> the
>>>>> transition of the structures I have. Anyone have suggestions?
>>>>>
>>>>> Thanks in advance,
>>>>> Jing
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>>>
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Received on Fri Sep 15 2023 - 11:30:03 PDT
