From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Wed Mar 11 2015 - 03:13:27 CDT
Check that you have the same PBCs defined in VMD as in the original
simulation.
On Wed, Mar 11, 2015 at 4:22 AM, Kevin C Chan <cchan2242-c_at_my.cityu.edu.hk>
wrote:
> Thanks! A simple "puts" works! So it loses its screen-out function inside a
> loop.
>
> I found weird things when I look at my outputs. When I feed coor and vel
> from a previous simulation (simulation-1) to a simulation-2, for which both
> simulations were turned on with the same colvar setting (a harmonic
> potential to dihedral value). I supposed the last dihedral value for the
> simulation-1 should be the same as the first value for the simulation-2 but
> it is not the case.
>
> I checked the logs and they should be reading the correct input coor and
> vel files. Using cv in VMD reading the coor file gives the first value of
> simulation-2 (again saying that simulation-2 is reading the correct coor
> file). And this value deviates a lot from the value I set with the center
> for the harmonic. However, inside the colvar.traj of simulation-1, it says
> my dihedral value is harmonically restrained to my desired value.
>
> Thanks in advance,
> Kevin
>
>
>
> On Wed, Mar 11, 2015 at 7:46 AM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
> > Hi Kevin, I think you will probably need:
> > puts [cv colvar dih value]
> > to see the value printed on the screen. Think of that command between
> > brackets as a measure command.
> >
> > You would need to recompile VMD if you load in multiple configurations
> > files. What you're using there should be fine with 1.9.2
> >
> >
> >
> > On Tue, Mar 10, 2015 at 7:13 PM, Kevin C Chan <
> cchan2242-c_at_my.cityu.edu.hk
> > > wrote:
> >
> >> Thanks to all of you and your replies. I got vmd1.9.2 and cv works
> >> horribly well.
> >>
> >> ***Except*** that I found my “cv” (shipped with
> >> vmd1.9.2-linux-opengl-cuda) just cannot run inside a for-loop:
> >> # I have loaded a number of frames and wanna compare their colvar
> values #
> >> cv molid top
> >> cv configfile dih.colvar
> >>
> >> for { set i 0 } { $i <= 9 } { incr i } {
> >> cv frame $i
> >> cv colvar dih update
> >> cv colvar dih value
> >> }
> >>
> >> By "cannot run" it means the vmd did not either give error messages or
> >> quit, instead just nothing happens.
> >>
> >> I noticed that Giacomo had given an update of colvars from Github but it
> >> seems I have to build my VMD from the source files especially all those
> >> libraries. I am just asking whether the update solves my problem of
> >> not-working-in-a-loop. If yes, I will go back and compile it. If no,
> what
> >> is it about actually?
> >>
> >> Thanks in advance,
> >> Kevin
> >>
> >> On 10 Mar, 2015, at 22:33, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> >> wrote:
> >>
> >> Kevin, you may want to try colvars inside VMD, calculating the variables
> >> without starting NAMD.
> >>
> >> I would recommend that you download and compile the source code of VMD,
> >> updating it with the colvars code from Github using the provided
> >> update-colvars-code.sh script:
> >>
> >> https://github.com/colvars/colvars/archive/master.zip
> >>
> >> Giacomo
> >>
> >> On Tue, Mar 10, 2015 at 3:24 PM, Kevin C Chan <
> >> cchan2242-c_at_my.cityu.edu.hk> wrote:
> >>
> >>> Thanks Josh!
> >>>
> >>> I am also wondering whether we can calculate such dihedral of 4 groups
> >>> simply using pdb+psf. Because right now I am doing with colvars turned
> on
> >>> and running few steps of a random MD and look at the colvars.traj and
> >>> honestly it is as stupid as it sounds.
> >>>
> >>> Thanks in advance,
> >>> Kevin
> >>>
> >>> On 10 Mar, 2015, at 22:14, Josh Vermaas <vermaas2_at_illinois.edu> wrote:
> >>>
> >>> Hi Kevin,
> >>>
> >>> I believe the way it is written is pretty standard, using the ordering
> >>> that folks use to describe dihedral potentials within molecules, and
> just
> >>> generalizing it to groups of atoms. So group1 would be first atom,
> group2
> >>> would be the second, and so on. The "dihedral" angle is measuring
> rotation
> >>> around the group2-group3 "bond" by measuring the angle between group1
> and
> >>> group4 if you are looking down the group2-group3 bond (Fig. 3 from the
> >>> Wikipedia article).
> >>>
> >>> -Josh Vermaas
> >>>
> >>> On 03/10/2015 06:52 AM, Kevin C Chan wrote:
> >>>
> >>> Thank you so much for the hint from "distance".
> >>>
> >>> Concerning the dihedral definition, I am not sure whether I get what
> you
> >>> are saying. In the Wikipedia, under the section "Dihedral angles of
> four
> >>> atoms
> >>> "
> >>> , it uses words like first atom, second atom and so on, so is this the
> >>> sequence that NAMD colvars are using for dihedral calculation?
> >>>
> >>>
> >>> Thanks, in advance,
> >>> Kevin
> >>>
> >>>
> >>>
> >>>
> >>> On Tue, Mar 10, 2015 at 7:28 PM, Giacomo Fiorin <
> >>> giacomo.fiorin_at_gmail.com> wrote:
> >>>
> >>>> The center of mass is not mentioned explicitly for all components,
> >>>> but these are all consistent with the distance:
> >>>>
> >>>>
> http://www.ks.uiuc.edu/Research/namd/2.10/ug/node57.html#SECTION000134110000000000000
> >>>> i.e. the groups' centers-of-mass are used to define individual points
>
-- Giacomo Fiorin Assistant Professor of Research Institute for Computational Molecular Science (ICMS) College of Science and Technology, Temple University 1925 North 12th Street (035-07), Room 704D Philadelphia, PA 19122-1801 Phone: +1-215-204-4213 https://icms.cst.temple.edu/members.html http://giacomofiorin.github.io/
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