[gmx-users] Re: trjconv -pbc nojump across multiple trajectories

Thu Nov 22 19:30:38 CET 2012

Hey Pablo,

Last frame from an .xtc file:

http://gromacs.5086.n6.nabble.com/How-to-get-the-number-of-frames-contained-by-an-xtc-trajectory-file-tp4998050p4998055.html

Cheers,

Tsjerk

On Thu, Nov 22, 2012 at 5:18 PM, Pablo Englebienne <p.englebienne at tudelft.nl
> wrote:

> Thanks for your reply, Tsjerk.
>
> Indeed, trjcat is a good option. I could first run "trjconv -pbc nojump"
> on a trajectory, then keep the last frame as a trr and stitch it with the
> following trajectory; trjconv then takes the first frame as reference for
> the nojump.
>
> Regarding this, what would be the easiest way to get the last frame out of
> the trajectory? I can think of using the output of gmxcheck to get the time
> of the last frame and then use it as the argument to "trjconv -b", but is
> there a simpler way?
>
> Regards,
> Pablo
>
>
> Dr. Pablo Englebienne
> Postdoctoral Researcher
>
> *TU Delft / 3mE / Process & Energy*
> /Engineering Thermodynamics (ETh) group/
>
> Building 46
> Leeghwaterstraat 44, room 030
> 2628 CA Delft
> The Netherlands
>
> *T* +31 (0)15 27 86662 <tel:+31152786662>
> *E* p.englebienne at tudelft.nl <mailto:p.englebienne at tudelft.**nl<p.englebienne at tudelft.nl>
> >
>
> On 11/22/2012 04:20 PM, gmx-users-request at gromacs.org wrote:
>
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>> Today's Topics:
>>
>>     1. Re: Re,i don't know how can i determine emtol (Ivan Gladich)
>>     2. top2psf with Amber99SB-ILDN (Steven Neumann)
>>     3. Re: top2psf with Amber99SB-ILDN (francesco oteri)
>>     4. Re: top2psf with Amber99SB-ILDN (Steven Neumann)
>>     5. Bonded parametrs for CG (Steven Neumann)
>>     6. trjconv -pbc nojump across multiple trajectories
>>        (Pablo Englebienne)
>>     7. Re: trjconv -pbc nojump across multiple trajectories
>>        (Tsjerk Wassenaar)
>>     8. On the usage of SD integrator as the thermostat (James Starlight)
>>
>>
>> ------------------------------**------------------------------**
>> ----------
>>
>> Message: 1
>> Date: Thu, 22 Nov 2012 12:17:50 +0100
>> From: Ivan Gladich <ivan.gladich at marge.uochb.cas.**cz<ivan.gladich at marge.uochb.cas.cz>
>> >
>> Subject: Re: [gmx-users] Re,i don't know how can i determine emtol
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Cc: Ali Alizadeh <ali.alizadehmojarad at gmail.com**>
>> Message-ID: <50AE09DE.5040805 at marge.uochb.**cas.cz<50AE09DE.5040805 at marge.uochb.cas.cz>
>> >
>> Content-Type: text/plain; charset=UTF-8; format=flowed
>>
>> On 11/21/2012 06:02 PM, Ali Alizadeh wrote:
>>
>>> 1- In your opinion, Can i simulate that system?
>>>>>
>>>> In my (humble) opinion:
>>>>
>>>> 1)Of course you can simulate that system...however  I doubt that,
>>>> without
>>>> starting from the exact initial configuration with the exactly same
>>>> set-up,
>>>> you can get the same results (i.e. see the nucleation).
>>>> The onset of ice nucleation is a random process and requires very long
>>>> simulation (the paper that you posted was analysing micro-second
>>>> trajectories!!).
>>>> There is the risk that you could try several different initial
>>>> configurations at several temperature without getting anything.
>>>>    However, read carefully that paper, I do not remember all the
>>>> details.
>>>>
>>>> If you are interested in ice crystal growth, I would suggest to start
>>>> with
>>>> an initial water/ice system: at temperature below the melting one you
>>>> will
>>>> see formation of new ice starting from the initial ice matrix.
>>>>
>>> I do not know how  can ice crystal in initial step, i study papers and
>>> i know ice , crystals formation and dissociation of crystals is very
>>> difficult,
>>> and we can use this method(as you said above) for melting or
>>> freezing(if i say correct)
>>>
>>> My problem is this case, how can i have a crystal in initial step,
>>>
>>>
>>>  You have three options
>>
>> 1) Surfing the web searching for some structure.
>>
>> 2)Try to implement the proton disordering algorithm of Buch et al.,
>> (V. Buch, P. Sandler and J. Sadlej, J. Phys. Chem. B, 1998, 102,
>> 8641âEUR"8653)
>>    which specifies orientations of water molecules such that ice
>> Ih BernalâEUR"Fowler constraints for each molecule are satisfied.
>> (J. D. Bernal and R. H. Fowler, J. Chem. Phys., 1933, 1, 515âEUR"548)
>>
>> 3) Someone kindly offer you his own structure, e.g.
>>
>> http://marge.uochb.cas.cz/~**gladich/Teaching.html<http://marge.uochb.cas.cz/~gladich/Teaching.html>
>>
>> (PS: This is the structure at O K...you have to heat it to the desired
>> temperature)
>> Good Luck
>> ivan
>>
>>
>>
>>  There are several works in literature on this.
>>>>
>>>>  2- How can i use rigid TIP4P model of water?
>>>>>
>>>> 2)  I would rather use other water model that have been explicitly
>>>> tested
>>>> for Ice
>>>>
>>>> (e.g. TIP4P/2005, TIP4P/Ice, TIP5P-Ew, NE6)
>>>>
>>> I think that i solved it, thank you,
>>>
>>>
>>>  Best
>>>> Ivan
>>>>
>>>>> Sincerely
>>>>>
>>>>> Ali Alizadeh
>>>>>
>>>>
>>>>
>>>> On 11/21/2012 09:43 AM, Ivan Gladich wrote:
>>>>
>>>>> Dear Ali
>>>>>       the paper that you are citing is using a rigid TIP4P water model
>>>>> As far as I know, emtol is relevant only for minimization or molecular
>>>>> dynamics with shell particle or flexible constraints.
>>>>> Therefore, as Justin told you, the emtol value should be irrelevant.
>>>>>
>>>>> Concerning this paper, I would like to warn you that h_omogeneous ice
>>>>> nucleation from bulk water_ with explicit water molecule is very rare
>>>>> event...
>>>>>
>>>>> It's depends from the initial condition and it requires very long
>>>>> simulations.
>>>>> Indeed, if I remember well this paper, they observed homogeneous ice
>>>>> crystal formation in only one of their trajectories...read carefully
>>>>> the
>>>>> paper!
>>>>>
>>>>> Best
>>>>> Ivan
>>>>>
>>>> --
>>> Sincerely
>>>
>>> Ali Alizadeh
>>>
>>
>>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada