Oh so it would create the bond between the two original molecules (across
the box) rather than the nearest image?
I am reluctant to do this because I need the approach to be done in "mass"
to a large amount of clusters. If this 'interesting' approach requires
visualization (or anything that requires human judgement), I won't be able
to apply it in these quantities.
Hmm, would you mind explaining why
- autoimage origin anchor:4
- center :4,5 origin
Isn't ideal? Would it not do what I want it to do?
Thanks so much,
Aseel
-----Original Message-----
From: Bill Ross [mailto:ross.cgl.ucsf.edu]
Sent: Saturday, August 12, 2017 4:04 PM
To: amber.ambermd.org
Subject: Re: [AMBER] Cpptraj to center molecules
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
>>
>>
>>
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>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
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