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.englebie...@tudelft.nl <mailto:p.englebie...@tudelft.nl>
On 11/22/2012 04:20 PM, gmx-users-requ...@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.glad...@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@gromacs.org>
Cc: Ali Alizadeh <ali.alizadehmoja...@gmail.com>
Message-ID: <50ae09de.5040...@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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