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
>
>
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--
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 Wed May 13 2020 - 23:30:02 PDT
