Re: colvars selecting frames

From: Stefano Guglielmo (stefano.guglielmo_at_unito.it)
Date: Tue Feb 20 2018 - 14:54:20 CST

Hi all,
thanks for sharing advices and opinions. In the end I opted for Worodm and
it worked fine.
Thanks again
Stefano

2018-02-01 17:42 GMT+01:00 Jérôme Hénin <jerome.henin_at_ibpc.fr>:

> Thinking about it, this could be a very simple feature to implement in
> CatDCD as well. If someone wants a quick little software project, it can be
> a feature request for CatDCD.
>
> Another option, certainly slower than Wordom, but working with any size of
> trajectory: write each frame separately as a 1-frame numbered DCD file,
> then cat everything with CatDCD. Ugly? Yes. Slow? You bet! Does the job? I
> think so.
>
> Jerome
>
> On 1 February 2018 at 17:21, Florian Blanc <blanc.flori_at_gmail.com> wrote:
>
>> 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>
>> 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
>>>>>> <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=>
>>>>>> ph. +39
>>>>>> <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=>
>>>>>> (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=>
>>>> ph. +39
>>>> <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=>
>>>> (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
>>
>>
>>
>

-- 
Stefano GUGLIELMO PhD
Assistant Professor of Medicinal Chemistry
Department of Drug Science and Technology
Via P. Giuria 9
10125 Turin, ITALY
ph. +39 (0)11 6707178

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