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
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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
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