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
> AMBER.ambermd.org
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_
> mailman_listinfo_amber&d=DwICAg&c=nE__W8dFE-shTxStwXtp0A&r=-GD698Wi4V6
> QX_wrQuVQ3g&m=20LfRjbPT5pG45UMK4hwAELKL8JMnHCY6shlM8F3YMc&s=2VwOyV3A3d
> 5ORrRFvnH2briLHIegcR6PBQ-6H8Ep4cA&e=
--
-------------------------
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
=DwICAg&c=nE__W8dFE-shTxStwXtp0A&r=-GD698Wi4V6QX_wrQuVQ3g&m=20LfRjbPT5pG45UM
K4hwAELKL8JMnHCY6shlM8F3YMc&s=R2gD4ypDg64becFQ8KfNyqAgaRdMD-aZTsg64CkSiqY&e=
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailma
n_listinfo_amber&d=DwICAg&c=nE__W8dFE-shTxStwXtp0A&r=-GD698Wi4V6QX_wrQuVQ3g&
m=20LfRjbPT5pG45UMK4hwAELKL8JMnHCY6shlM8F3YMc&s=2VwOyV3A3d5ORrRFvnH2briLHIeg
cR6PBQ-6H8Ep4cA&e=
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Aug 12 2017 - 13:00:02 PDT
