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

Pablo Englebienne p.englebienne at tudelft.nl
Thu Nov 22 17:18:22 CET 2012

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?


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>

On 11/22/2012 04:20 PM, gmx-users-request at gromacs.org wrote:
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>     1. Re: Re,i don't know how can i determine emtol (Ivan Gladich)
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>     4. Re: top2psf with Amber99SB-ILDN (Steven Neumann)
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>     6. trjconv -pbc nojump across multiple trajectories
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>     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>
> 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>
> 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
> (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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