Re: colvars selecting frames

From: Florian Blanc (blanc.flori_at_gmail.com)
Date: Thu Feb 01 2018 - 10:21:18 CST

Dear all,

I am not sure if I understand Stefano's problem, but the Wordom tool
provides a single command line to perform extraction of a user-defined
series of frames to a single dcd. After downloading and installing
wordom (http://wordom.sourceforge.net/), write the list of desired frame
numbers in a text file (e.g. framelist.txt) and use the following command:

wordom -F framelist.txt -imol my_system.pdb -itrj my_traj.dcd -otrj
my_output_traj.dcd

I use this function on a regular basis and it is usually significantly
faster than VMD to process trajectory files.

Hope that helps,

Florian

On 02/01/2018 05:03 PM, Giacomo Fiorin wrote:
> Hi Stefano, a line-by-line review of code from the mailing list would
> be impractical.
>
> If your trajectory fits all in the memory of VMD I would go with
> Jérôme's suggestion, which is the most convenient in any case where
> you want to extract some frames from the trajectory based on some
> quantity (e.g. not just a collective variable).
>
> If you have a GROMACS installation available, have a look at the -drop
> flag of gmx trjconv, which can filter an existing trajectory based on
> the value of a quantity read from a corresponding .xvg file.  The .xvg
> file doesn't have to have Xmgrace formatting headers, it can be a
> plain text file: GROMACS only needs the .xvg extension so that it can
> rely on a standardized file extension for text files with data.  You
> can manipulate the .colvars.traj file written by NAMD if it has the
> same frequency as the DCD file, or just change your script to write
> that file.
>
> There was a way in the past to load VMD/molfile plugins in trjconv and
> load DCD files directly, but I haven't found documentation for it in
> recent GROMACS versions.  In the worst case scenario, just convert
> your trajectories to .trr with VMD before running them through GROMACS.
>
> Giacomo
>
>
> On Thu, Feb 1, 2018 at 7:32 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr
> <mailto:jerome.henin_at_ibpc.fr>> wrote:
>
> true, i's probably not trivial to write out a custom selection of
> frames to a file. The easiest I can think of is to go through all
> the frames backwards from the end, and delete those you don't
> want. Then write those that are left. The point of starting from
> the end is that the frame numbers don't change when you delete
> later frames.
>
> Jerome
>
> On 1 February 2018 at 13:06, Stefano Guglielmo
> <stefano.guglielmo_at_unito.it <mailto:stefano.guglielmo_at_unito.it>>
> wrote:
>
> Jerome, thanks for hint.
> I must say that I'm far from being expert in scripting; I
> tried the following one, but it just write one frame in the
> output dcd file. Is somebody that patient to provide some more
> suggestions?
>
> Thanks in advance
> Stefano
>
> package require bigdcd
> proc metadynamics_colvars { frame } {
>      global all
>      if {$frame == 1} {
>      cv molid 0
>      cv configfile colvar4.txt
>      cv load cdk_8bS_cv4_replica1_250.restart
> }
>      cv update
>       set energy [cv bias metadynamics1 energy]
>       set dist [cv colvar Dist value]
>       set sel [atomselect top all]
>       set n [molinfo top get numframes]
>       #set ang [cv colvar angle value]
>       if { $dist > 15 } {
>      if { $energy > 8 } {
>             for { set i 0 } { $i < $n } { incr i } {
>   $sel frame $i
>   $sel update
>   animate write dcd cdk2_8bS_min.dcd $sel
>         }
>             }
>           }
>  }
>  set mol [mol new cdk2_8bS_pocket_wb_ion.psf type psf waitfor all]
>  set all [atomselect $mol all]
>  $all global
>  bigdcd metadynamics_colvars auto cdk_8bS_cv4_210.dcd
>  bigdcd_wait
>  quit
>
> 2018-01-31 10:22 GMT+01:00 Jérôme Hénin <jerome.henin_at_ibpc.fr
> <mailto:jerome.henin_at_ibpc.fr>>:
>
> Dear Stefano,
>
> You can do that with a VMD script using the colvars interface.
>
> Best,
> Jerome
>
> On 31 January 2018 at 02:37, Stefano Guglielmo
> <stefano.guglielmo_at_unito.it
> <mailto:stefano.guglielmo_at_unito.it>> wrote:
>
> Dear all,
> I was wondering if it is possible to select and
> ouput/save frames having collective variable values in
> a user defined range (or in alternative metadynamics
> energy value) out of a metadynamics trajectory
> obtained with the colvars module in NAMD.
> Thanks in advance
> Stefano
>
> --
> Stefano GUGLIELMO PhD
> Assistant Professor of Medicinal Chemistry
> Department of Drug Science and Technology
> Via P. Giuria 9
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>
> --
> Stefano GUGLIELMO PhD
> Assistant Professor of Medicinal Chemistry
> Department of Drug Science and Technology
> Via P. Giuria 9
> <https://urldefense.proofpoint.com/v2/url?u=https-3A__maps.google.com_-3Fq-3DVia-2BP.-2BGiuria-2B9-2B10125-2BTurin-2C-2BITALY-2B-253Chttps-3A__maps.google.com_-3Fq-253DVia-252BP.-252BGiuria-252B9-252B10125-252BTurin-2C-252BITALY-252Bph.-252B-25252B39-2526entry-253Dgmail-2526source-253Dg-253E-2Bph.-2B-252B39-2B-253Chttps-3A__maps.google.com_-3Fq-253DVia-252BP.-252BGiuria-252B9-252B10125-252BTurin-2C-252BITALY-252Bph.-252B-25252B39-2526entry-253Dgmail-2526source-253Dg-253E-26entry-3Dgmail-26source-3Dg&d=DwMFaQ&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=jUfnSyKkfkyVRBIUzlG1GSGGZAZGcznwr8YliSSCjPc&m=c-AT7vCwTf0NHLjMmJZpSRY91EWDj9NEY7NMltNYPQY&s=r-5fHj6nN4lIE6CW6U-pIO8uW0Ffi9bCs1Nyl4qZOfg&e=>
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>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin <https://github.com/giacomofiorin>

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