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">&lt;<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>&gt;</span> wrote:<br>
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<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>
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On Wed, Jun 17, 2009 at 5:20 PM, Justin A. Lemkul &lt;<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt; 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>
<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> &lt;<a href="http://vt.edu" target="_blank">http://vt.edu</a>&gt; | (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>
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>
========================================<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>