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
>>>>
>>>
>>
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>
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Received on Sat Jul 08 2017 - 21:30:02 PDT
