From: Kevin C Chan (cchan2242-c_at_my.cityu.edu.hk)
Date: Wed Mar 11 2015 - 05:03:54 CDT
For the cv calculation I just loaded the coor files so no PBC parameters
were inserted. However as it gives exactly the first value of simulation-2
so I assumed it plays well with the PBC. I have been looking at my protein,
it has never gone out of the water box.
Nevertheless cv calculation in VMD is just one of the checkings. The
problem relies on why would I have two different values between the end of
simulation-1 and the start of simulation-2. They should be loading very
similar coor, vel and xsc files (though not exactly the same as I used to
load the restart ones).
For your information, the last number of simulation-1 has way earlier
coupled to my desired value, say 10, and the first value of simulation-2 is
maybe 30 and then it starts to be coupled towards the desired value. As I
am doing a number of subsequent simulations, I can see every colvars.traj
is like this.
Once again, many thanks in advance!
Kevin
On Wed, Mar 11, 2015 at 4:13 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:
> 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/
>
>
This archive was generated by hypermail 2.1.6 : Tue Dec 27 2016 - 23:20:57 CST