Instead of an energy function, you could add up all the atom pair distances.
Bill
On 7/8/17 9:00 PM, Bill Ross wrote:
> Hi Guqin,
>
> Maybe it could be a python script. E.g. start with the first molecule's
> position as the reference. Then somehow for each other molecule
> recursively choose a translation (or none) from the neighboring images,
> finally when all molecules have been recursively assigned, calculate the
> energy with an available? amber call, storing the min config seen in a
> global variable. It could be parallelizable. Ok time-wise for a few
> molecules, but I wouldn't want to do it with the waters in a bath.
>
> Bill
>
>
>
> On 7/8/17 8:34 PM, Guqin Shi wrote:
>> Hi Bill,
>>
>> Could you explain a little bit more about "image minimizer"...my
>> understanding is to write a small script that try all different orders of
>> center-image...?
>>
>> Best,
>> Guqin
>>
>> On Sat, Jul 8, 2017 at 10:22 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>>
>>> What's needed is an image minimizer that tries all neighboring box
>>> placements for all molecules.
>>>
>>> Bill
>>>
>>>
>>> On 7/8/17 7:06 PM, Guqin Shi wrote:
>>>> Hi Dan,
>>>>
>>>> Thanks for reply.
>>>> Yes, the first I've thought of is to use "autoimage" directly. I have to
>>>> admit it worked unexpectedly well. But for the late ns trajectories, it
>>>> failed, too. It has the same result as the one I got from the separate
>>>> center-and-image...
>>>>
>>>> Best,
>>>> Guqin
>>>>
>>>> On Sat, Jul 8, 2017 at 8:02 PM, Daniel Roe <daniel.r.roe.gmail.com>
>>> wrote:
>>>>> Hi,
>>>>>
>>>>> Try the 'autoimage' command in cpptraj and see if that works for you.
>>>>>
>>>>> -Dan
>>>>>
>>>>> On Sat, Jul 8, 2017 at 6:59 PM Guqin Shi <shi.293.osu.edu> wrote:
>>>>>
>>>>>> Dear all,
>>>>>>
>>>>>> My simulation is on a huge complex containing 6 molecules. To visualize
>>>>> the
>>>>>> trajectory and get "correct" coordinates, I usually center-n-image the
>>>>>> coordinates... I used to center on 1 molecule, image, and then center
>>> on
>>>>> 2
>>>>>> molecules (include the first one), and then image; and eventually
>>> center
>>>>> on
>>>>>> 6 molecules and image, as suggested in some amber mailing list posts.
>>> It
>>>>>> worked well.
>>>>>>
>>>>>> ex.
>>>>>> center :1-300 origin (molecule 1)
>>>>>> image center origin
>>>>>> center :1-500 origin (molecule 2)
>>>>>> image center origin
>>>>>> center :1-650 origin (molecule 3)
>>>>>> image center origin
>>>>>> center :1-950 origin (molecule 3)
>>>>>> image center origin
>>>>>> center :1-1150 origin (molecule 4)
>>>>>> image center origin
>>>>>> center :1-1300 origin (molecule 6)
>>>>>> image center origin
>>>>>>
>>>>>> However, as the molecules deviates during the simulation, after
>>> applying
>>>>>> the above commands, there is always one molecule (it could be different
>>>>>> molecule dependent on the order I center-image on different masks...)
>>>>> that
>>>>>> just couldn't be placed back... no matter how different combinations I
>>>>> have
>>>>>> tried...
>>>>>>
>>>>>> My first question is that does it make sense that the above commands
>>> work
>>>>>> well for first quite a few ns of trajectories but failed to wrap for
>>> the
>>>>>> late ns of trajectories...?
>>>>>>
>>>>>> The second one will be if there is any tips or suggestions or starting
>>>>>> point that I could try out? I have tried different combinations,
>>> starting
>>>>>> center on different molecule(s), I just couldn't get all 6 back to the
>>>>>> correct place...
>>>>>>
>>>>>> I also tried to center on reference structure...but it just put
>>> molecule
>>>>>> onto the geometric center, the direction is still off...I don't know
>>> how
>>>>> to
>>>>>> center molecules onto a suitable place so that all 6 could be fit into
>>>>> one
>>>>>> box...That doesn't make sense...I mean I start with an intact
>>> complex...
>>>>>> Thank you for any thoughts!
>>>>>> Best,
>>>>>> Guqin
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Guqin SHI
>>>>>> PhD Candidate in Medicinal Chemistry and Pharmacognosy
>>>>>> College of Pharmacy
>>>>>> The Ohio State University
>>>>>> Columbus, OH, 43210
>>>>>> _______________________________________________
>>>>>> AMBER mailing list
>>>>>> AMBER.ambermd.org
>>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>>
>>>>> --
>>>>> -------------------------
>>>>> Daniel R. Roe
>>>>> Laboratory of Computational Biology
>>>>> National Institutes of Health, NHLBI
>>>>> 5635 Fishers Ln, Rm T900
>>>>> Rockville MD, 20852
>>>>> https://www.lobos.nih.gov/lcb
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>
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Received on Sat Jul 08 2017 - 21:30:03 PDT
