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: [EMAIL PROTECTED] [EMAIL PROTECTED] >> On Behalf Of Vasilii Artyukhov [EMAIL PROTECTED] >> 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 >> <[EMAIL PROTECTED]<mailto:[EMAIL PROTECTED]>>: >> 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 >> >> >> _______________________________________________ >> gmx-users mailing list >> gmx-users@gromacs.org<mailto:gmx-users@gromacs.org> >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to >> [EMAIL PROTECTED]<mailto:[EMAIL PROTECTED]>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- ------------------------------------------------------ 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: [EMAIL PROTECTED] Skype: ran.friedman ------------------------------------------------------ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
