Hi, Amanda
As Kellon mentioned, I think you missed setting infe=1 in your mdin,
you can double check in your mdout output, there should be information
printed out
if the COM angles are read in.
Feng
On Thu, May 14, 2020 at 3:04 PM Kellon Belfon <kellonbelfon.gmail.com>
wrote:
> 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
> > > _______________________________________________
> > > AMBER mailing list
> > > 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
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> > _______________________________________________
> > AMBER mailing list
> > 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
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Feng Pan
PostDoc
Florida State University
Department of Statistics
Email: fpan3.ncsu.edu; fpan.fsu.edu
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 18 2020 - 07:00:02 PDT
