[gmx-users] water can't freeze

[Erik Marklund]

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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-- 
-----------------------------------------------
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 4537        fax: +46 18 511 755
erikm at xray.bmc.uu.se    http://xray.bmc.uu.se/molbiophys