Dear Justin:<br><br>Thank you so much for your answer. That helps a lot!<br><br><div class="gmail_quote">On Thu, Jun 18, 2009 at 10:35 AM, 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 class="im"><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 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>
</blockquote>
<br></div>
That is one of the known problems with using cut-off, yes.<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><div></div><div class="h5">
On Wed, Jun 17, 2009 at 5:20 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
  Yanmei Song wrote:<br>
<br>
    Dear Users:<br>
<br>
    I was running a system by non-equilibrium MD using a plain<br>
    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<br>
    system is 303.54 after 5ns run ( the temperature turns to 303 in<br>
    500ps). Thanks for the help in advance!<br>
<br>
<br>
  Why are you using cutoff for coulombtype?  It is the reason for the<br>
  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>
    --     Yanmei Song<br>
    Ph.D. Candidate<br>
    Department of Chemical Engineering<br>
    Arizona State University<br>
<br>
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<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></div>
  jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><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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<br>
<br>
<br>
<br>
-- <br>
Yanmei Song<br>
Ph.D. Candidate<br>
Department of Chemical Engineering<br>
Arizona State University<br>
</div></blockquote><div><div></div><div class="h5">
<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>
<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Yanmei Song<br>Ph.D. Candidate<br>Department of Chemical Engineering<br>Arizona State University<br>