'Interesting' includes creating all the requisite 0-force angle/torsion
potentials to go with the fake bond.
Bill
On 8/12/17 1:04 PM, Bill Ross wrote:
> I'm not recommending this, but an interesting hack would be to create a
> forceless bond between the two molecules of interest, to fool autoimage.
> But with this approach, and no matter how you achieve the effect, you
> will have to settle for the initial relative positions of the two
> molecules, which may not always be what you want.
>
> Bill
>
>
> On 8/12/17 12:55 PM, Aseel Bala Ahmed wrote:
>> Neat!
>> However, would this center only molecule 4?
>> I am looking to center the entire hydrogen bonded cluster (i.e. molecules 4
>> and 5prime).
>>
>> When I use: autoimage origin anchor :4,5
>> I get an error:
>> Error: Anchor mask [:4,5] corresponds to 2 mols, should only be 1.
>>
>> Which tells me I could only use the command with one molecule.
>>
>> Would a way around this be to use
>> autoimage origin anchor:4
>> center :4,5 origin
>>
>> to first wrap and find images and then center the whole cluster?
>>
>> Thanks very much for your help.
>> Best,
>> Aseel
>>
>> -----Original Message-----
>> From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
>> Sent: Saturday, August 12, 2017 1:50 PM
>> To: AMBER Mailing List <amber.ambermd.org>
>> Subject: Re: [AMBER] Cpptraj to center molecules
>>
>> Hi,
>>
>> On Fri, Aug 11, 2017 at 3:36 PM, Aseel Bala <balaahme.msu.edu> wrote:
>>> However, I am running into an issue when 4 is on one edge of the frame
>>> and 5 is on the other edge. In these situations, 4 is actually
>>> H-bonded to an 'image' of 5 produced by the periodic boundary
>>> condition. Let's call this image 5prime.
>> What you are describing is an imaging artifact, and is very common in MD
>> simulations with PBC and coordinate wrapping. The 'autoimage'
>> command was designed to handle this kind of situation. Instead of 'center'
>> and 'image', try:
>>
>> autoimage origin anchor :4
>>
>> Hope this helps,
>>
>> -Dan
>>
>> PS - FYI the 'hbond' command in cpptraj now handles imaging natively via the
>> 'image' keyword.
>>
>>>
>>> In this case, cpptraj actually centers 4 and 5 instead of 4 and 5prime.
>>>
>>>
>>>
>>> Is there a way that cpptraj can be used to center a molecule and the
>>> closest image of another molecule to it? So that I would be able to
>>> have 4 and 5prime in the center?
>>>
>>>
>>>
>>> Thank you very much in advance!
>>>
>>>
>>>
>>> --
>>>
>>>
>>>
>>> Aseel M. Bala
>>>
>>> Michigan State University
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
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>>
>> --
>> -------------------------
>> Daniel R. Roe
>> Laboratory of Computational Biology
>> National Institutes of Health, NHLBI
>> 5635 Fishers Ln, Rm T900
>> Rockville MD, 20852
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__www.lobos.nih.gov_lcb&d
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Received on Sat Aug 12 2017 - 13:30:03 PDT
