Dear Justin:<br><br>Thanks for your response.<br><br>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?<br>
<br><div class="gmail_quote">On Wed, Jun 17, 2009 at 5:20 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div></div><div class="h5"><br>
<br>
Yanmei Song wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Users:<br>
<br>
I was running a system by non-equilibrium MD using a plain Cut-off for the electrostatics:<br>
<br>
title = water<br>
cpp = /lib/cpp<br>
constraints = all_bonds<br>
integrator = md<br>
dt = 0.004 ; ps !<br>
nsteps = 500000 ; total 8ns.<br>
nstcomm = 1<br>
nstxout = 50000<br>
nstvout = 50000<br>
nstfout = 0<br>
nstlog = 5000<br>
nstenergy = 5000<br>
nstxtcout = 25000<br>
nstlist = 10<br>
ns_type = grid<br>
pbc = xyz<br>
coulombtype = Cut-off<br>
rlist = 0.8<br>
rcoulomb = 0.9<br>
rvdw = 0.8<br>
fourierspacing = 0.12<br>
ewald_rtol = 1e-5<br>
;nemd<br>
cos_acceleration = 0.005<br>
; Berendsen temperature coupling is on in two groups<br>
Tcoupl = berendsen<br>
tc_grps = SOL<br>
tau_t = 0.1<br>
ref_t = 300<br>
; Energy monitoring<br>
energygrps = SOL<br>
; Isotropic pressure coupling is now on<br>
Pcoupl = berendsen<br>
pcoupltype = isotropic<br>
;pc-grps = SOL<br>
tau_p = 1.0<br>
ref_p = 1.0<br>
compressibility = 4.5e-5<br>
<br>
; Generate velocites is off at 300 K.<br>
gen_vel = yes<br>
gen_temp = 300.0<br>
gen_seed = 100000<br>
<br>
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!<br>
</blockquote>
<br></div></div>
Why are you using cutoff for coulombtype? It is the reason for the heating you are seeing:<br>
<br>
<a href="http://oldwww.gromacs.org/pipermail/gmx-users/2009-February/039505.html" target="_blank">http://oldwww.gromacs.org/pipermail/gmx-users/2009-February/039505.html</a><br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div class="im">
-- <br>
Yanmei Song<br>
Ph.D. Candidate<br>
Department of Chemical Engineering<br>
Arizona State University<br>
<br>
<br></div>
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</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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</blockquote></div><br><br clear="all"><br>-- <br>Yanmei Song<br>Ph.D. Candidate<br>Department of Chemical Engineering<br>Arizona State University<br>