Yanmei Song wrote:
Dear Justin:
Thanks for your response.
The reason I am doing this is that I wanted to test what the different
electrostatics treatments will affect my results. So the heating up is
normal by using a plain cut-off and the results can not be trusted, right?
On Wed, Jun 17, 2009 at 5:20 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
That is correct. Check J. Chem. Theor. Comp. 2 (2006) p. 1-11.
Yanmei Song wrote:
Dear Users:
I was running a system by non-equilibrium MD using a plain
Cut-off for the electrostatics:
title = water
cpp = /lib/cpp
constraints = all_bonds
integrator = md
dt = 0.004 ; ps !
nsteps = 500000 ; total 8ns.
nstcomm = 1
nstxout = 50000
nstvout = 50000
nstfout = 0
nstlog = 5000
nstenergy = 5000
nstxtcout = 25000
nstlist = 10
ns_type = grid
pbc = xyz
coulombtype = Cut-off
rlist = 0.8
rcoulomb = 0.9
rvdw = 0.8
fourierspacing = 0.12
ewald_rtol = 1e-5
;nemd
cos_acceleration = 0.005
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc_grps = SOL
tau_t = 0.1
ref_t = 300
; Energy monitoring
energygrps = SOL
; Isotropic pressure coupling is now on
Pcoupl = berendsen
pcoupltype = isotropic
;pc-grps = SOL
tau_p = 1.0
ref_p = 1.0
compressibility = 4.5e-5
; Generate velocites is off at 300 K.
gen_vel = yes
gen_temp = 300.0
gen_seed = 100000
I can not figure out where I did wrong, the temperature of the
system is 303.54 after 5ns run ( the temperature turns to 303 in
500ps). Thanks for the help in advance!
Why are you using cutoff for coulombtype? It is the reason for the
heating you are seeing:
http://oldwww.gromacs.org/pipermail/gmx-users/2009-February/039505.html
-Justin
--
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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--
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
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David.
________________________________________________________________________
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Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
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