Re: colvars selecting frames

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Feb 01 2018 - 10:03:14 CST

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> 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
> > 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>:
>>
>>> 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> 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
>>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__maps.google.com_-3Fq-3DVia-2BP.-2BGiuria-2B9-2B10125-2BTurin-2C-2BITALY-2Bph.-2B-252B39-26entry-3Dgmail-26source-3Dg&d=DwMFaQ&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=jUfnSyKkfkyVRBIUzlG1GSGGZAZGcznwr8YliSSCjPc&m=c-AT7vCwTf0NHLjMmJZpSRY91EWDj9NEY7NMltNYPQY&s=3E7jptP47i1qtTQkeE8C5EEXHEj7ERp7-fQviSYguB4&e=>
>>>> 10125 Turin, ITALY
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>>>> (0)11 6707178
>>>>
>>>>
>>>
>>
>>
>> --
>> 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=>
>> 10125 Turin, ITALY
>> <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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>> (0)11 6707178
>>
>>
>

-- 
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

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