[gmx-users] water can't freeze

[Ran Friedman]

There are several different crystal phases of water. For simulation
setup, it's best (always, not only with freezing of water) to check the
literature. This will also give you a hint on what have already been
done. Quite a few MD simulations of ice were reported. If you have a
good idea on what you want to see, verify that it hasn't already been
performed.

Ran.

Erik Marklund wrote:
> I think you'll have to do it manually. The geometry for ice shouldn't
> be too hard to find, and with that you can build your own coordinate
> file for a chunk of ice. Ice is not the only nucleating agent for
> water freezing though. In large scale nucleation protocols some silver
> compound is used if I remember correctly. Still, nucleation reactions
> are generally pretty slow in comparison to melting, so don't expect to
> see much happening in the first hundreds of ps.
>
> /Erik
>
> Wei, Xiupeng skrev:
>> Dear Vasilii and other users,
>>           Thanks for you reply.
>>           I triedto do the simulation you said.   But how to setup
>> the initial configuration which is putting water contacting with ice,
>> I knew in Gms tutor there is a example of mixed water and mathenol,
>> it is a water box contacting with a mathenol box. I searched mailing
>> list and wikki, however, no useful information to create such a
>> configuration. Would you give me some suggestions?
>>          Does it still use editconf and genbox to create it?
>>
>> Best regards,
>> xiupeng
>> ________________________________________
>> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org]
>> On Behalf Of Vasilii Artyukhov [darth.vasya at gmail.com]
>> Sent: Saturday, April 19, 2008 12:17 PM
>> To: Discussion list for GROMACS users
>> Subject: Re: [gmx-users] water can't freeze
>>
>> Dear Xiupeng,
>>
>> What you're seeing is the difference between freezing water and
>> overcooling it. If you want your water to crystallize, you'll
>> actually have to make it - e.g., by putting it in contact with ice.
>> Normally, pure water doesn't freeze on its own, you can easily verify
>> this experimentally at home :)
>>
>> Best regards,
>> Vasilii
>>
>> 2008/4/19, Wei, Xiupeng
>> <xiupeng-wei at uiowa.edu<mailto:xiupeng-wei at uiowa.edu>>:
>> Hi gmx users,
>>          I'm a new Gromacs user. Till now, I can get pretty good
>> simulation of ice melting to water, but why can't I simulate water
>> freezing to ice?
>>          The .top and .gro files used for water freezing simulation
>> are generated by ice melting to 310K. I changed the temperature in
>> .mdp file to 230K, but after mdrun, the water was still water, it
>> can't freeze?
>>          How can I get water freezing to ice?
>>         I paste mdp for your reference.
>>         Thanks.
>>
>> best,
>> xiupeng
>>
>>
>> title                    = icing at 230 K with cuffoff
>> cpp                      = /lib/cpp
>> integrator               = md
>> ;Time step
>> dt                       = 0.002
>> nsteps                   = 100000
>> ;Output control
>> nstxout                  = 100000
>> nstvout                  = 100000
>> nstlog                   = 100
>> nstenergy                = 100
>> nstxtcout                = 100
>> ;Neigbour searching
>> nstlist                  = 10
>> ns_type                  = grid
>> rlist                    = 0.8
>> ;Non bonded interaction
>> coulombtype              = pme
>> optimize_fft             = yes
>> fourierspacing           = 0.2
>> pme-order                = 6
>> ewald-rtol               = 1e-05
>> rcoulomb                 = 0.8
>> vdw-type                 = Cut-off
>> rvdw                     = 0.8
>> DispCorr                 = EnerPres
>> ;Temperature coupling
>> tcoupl                   = berendsen
>> tc-grps                  = System
>> tau_t                    = 0.1
>> ref_t                    = 230
>> ;Pressure coupling
>> pcoupl                   = berendsen
>> pcoupltype               = isotropic
>> tau_p                    = 1.0
>> compressibility          = 5e-5
>> ref_p                    = 1.0
>>
>> gen_temp                 = 230.0
>> constraints              = all-bonds
>> ; generate velocities
>> gen_vel                  = yes
>> gen_seed                 = 173529
>>
>>
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>
>


-- 
------------------------------------------------------
Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman
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