If you think about your angle being formed between two vectors that
intersect at a common point aka the vertex of the angle, then as long as
the group defining your vertex is in the middle (or the second group) then
you should be fine.
So in your example, the group in the middle will be your group defining the
vertex (5118,5*137*,5153,)
On Thu, May 14, 2020 at 2:19 AM Amanda Buyan <Amanda.Buyan.anu.edu.au>
wrote:
> Hi Kellon,
>
> I'm using Amber18. The 0137 is a type; it should be 5137 - whoops!
>
> Could you also tell me what order my atomgroups should be in for COM_ANGLE?
>
> I'm trying again with cv_ni=17
>
>
> Best wishes
>
>
> Amanda
>
> ________________________________
> From: Kellon Belfon <kellonbelfon.gmail.com>
> Sent: 14 May 2020 12:34
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Steered MD with COM_ANGLE
>
> Hi,
>
> Which version of Amber are you using?
>
> The *0137* in your cv file. Is that intended?
> cv_i = 51401,51415,51421,51436,51446,0,5118,*0137*
> ,5153,0,6215,6236,6246,7999,8015,8031,0,
> your cv_ni should be 17 since you have 17 elements in cv_i
> Do you have infe=1 set in your input file?
>
> Everything else looks okay to me.
>
> If you have amber20, there is also the option of using COM angle for the
> nmropt=1 with ifvari option if you are interested?
>
> On Wed, May 13, 2020 at 7:43 PM Amanda Buyan <Amanda.Buyan.anu.edu.au>
> wrote:
>
> > Hi Adrian,
> >
> > Yes, I've already corrected for this, but thanks for checking!
> >
> > What other data would you need from me to help me? I've provided my
> > collective variable file that I've been using for Steered MD; what else
> > would you need?
> >
> > Amanda
> >
> > ________________________________
> > From: Adrian Roitberg <roitberg.ufl.edu>
> > Sent: 14 May 2020 09:36
> > To: amber.ambermd.org <amber.ambermd.org>
> > Subject: Re: [AMBER] Steered MD with COM_ANGLE
> >
> > We might more data or even look at your code, but for starters, VMD
> > starts counting atoms from 0 and amber from 1. Maybe you already
> > corrected for this, but it is something that happens quite a bit.
> >
> > Adrian
> >
> >
> > On 5/13/20 7:32 PM, Amanda Buyan wrote:
> > > [External Email]
> > >
> > > Hi everyone,
> > >
> > > I am trying to do a Steered MD simulation, where I am calculating the
> > centre of mass of an angle between three atom groups. I've already
> checked
> > in VMD to see that the indices I am using for the atoms are correct.
> When
> > I run with the following input file, I don't get any movement of the
> > collective variable:
> > >
> > > ----
> > > cv_file
> > > &colvar
> > > cv_type = 'COM_ANGLE'
> > > cv_ni = 14,
> > > ! | one vertex |
> > middle | second vertex |
> > > cv_i =
> >
> 51401,51415,51421,51436,51446,0,5118,0137,5153,0,6215,6236,6246,7999,8015,8031,0,
> > > nharm = 1,
> > > harm = 30.0,
> > > npath = 2,
> > > path = 20.0,120.0,
> > > path_mode = 'LINES',
> > > /
> > > ----
> > >
> > > do I have everything correct (I don't normally have the comment in
> there
> > - I put it in for easy reference? Could it be something as simple as
> wrong
> > atom selections, even though I've checked those twice? The Amber manual
> is
> > also not clear about the ordering of the three atom groups, so I'm unsure
> > if I have that right...
> > >
> > > Best wishes
> > >
> > > Amanda
> > >
> > >
> > >
> > > Dr. Amanda Buyan
> > >
> > > Postdoctoral Fellow, Corry Lab
> > >
> > > Research School of Biology
> > >
> > > 134 Linnaeus Way
> > >
> > > Canberra, ACT 2601
> > >
> > > amanda.buyan.anu.edu.au
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > >
> >
> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=sJ6xIWYx-zLMB3EPkvcnVg&r=dl7Zd5Rzbdvo14I2ndQf4w&m=q9D6mAgFwFUnw7lktFqC2mn184jJmNIN5jhpkFsniZw&s=YyBszKcdNnVyv9dz1XLelcMwTh5LMHjVtr548JShir8&e=
> >
> > --
> > Dr. Adrian E. Roitberg
> > V.T. and Louise Jackson Professor in Chemistry
> > Department of Chemistry
> > University of Florida
> > roitberg.ufl.edu
> > 352-392-6972
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Kellon A. A. Belfon, Graduate Student
> Carlos Simmerling Laboratory
> The Laufer Center for Physical and Quantitative Biology
> The Department of Chemistry, Stony Brook University
> Stony Brook, New York 11794
> Phone: (347) 546-4237 <(347)+546+4237> Email: kellon.belfon.stonybrook.
> <kellon.belfon.stonybrook.edu>edu
> _______________________________________________
> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Kellon A. A. Belfon, Graduate Student
Carlos Simmerling Laboratory
The Laufer Center for Physical and Quantitative Biology
The Department of Chemistry, Stony Brook University
Stony Brook, New York 11794
Phone: (347) 546-4237 <(347)+546+4237> Email: kellon.belfon.stonybrook.
<kellon.belfon.stonybrook.edu>edu
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Received on Thu May 14 2020 - 12:30:02 PDT
