Dear users,<br><br>I am using the Reaction-Field method for electrostatics interactions. <span id="result_box" class="short_text" lang="en"><span class="hps">I used</span> <span class="hps">the following parameters for all input files (em.mdp, pr.mdp, nvt.mdp, npt.mdp, md.mdp). I just changed as an </span></span>epsilon_rf=78 in md.mdp. If I set nstlist=rlist=rcoulomb=rvdw=1.0 for energy minimization, would not it be better? <span id="result_box" class="short_text" lang="en"><span class="hps">What is</span> <span class="hps">your</span> <span class="hps">suggestions?</span></span><br>
<br>; Neighbor Searching Parameters<br>
nstlist                 = 5  <br>
ns-type                 = Grid        <br>
pbc                = xyz            <br>
rlist                   = 0.9      <br>

; Electrostatics<br>
coulombtype             = Reaction-Field  <br>
rcoulomb                = 1.4          <br>
epsilon_rf              = 54            <br>

; VdW<br>
vdw-type                = Cut-off          <br>
rvdw                    = 1.4            <br><b><br>Another question:</b> I used 200 K (in pr.mdp) and 300 K (in nvt.mdp, npt.mdp and md.mdp) the reference temperature for coupling. I analysed the temperature after production run. 


        
        
        
        I get &quot;Temperature=312.646&quot; 

(g_energy -f md.edr -o temperature.xvg). that is, <span id="result_box" class="" lang="en"><span class="hps">The temperature</span> <span class="hps">has increased</span> (</span><span id="result_box" class="short_text" lang="en"><span class="hps">approximately 12 K)</span></span><span id="result_box" class="" lang="en"> <span class="hps">during the</span> <span class="hps">simulation</span></span>. <span id="result_box" class="" lang="en"><span class="hps">What could be the</span> <span class="hps">reason for</span> <span class="hps">the increase in</span> <span class="hps">temperature</span><span class="">?</span></span> I had setted to 200 K the reference temperature for coupling in pr.mdp.<span id="result_box" class="short_text" lang="en"><span class="hps"> it</span> <span class="hps">can cause</span><span class="">?</span></span><br>
<br>My em.mdp file <span id="result_box" class="short_text" lang="en"><span class="hps">is as the following:</span></span><br><u><b>em.mdp:</b></u><br>title                = Energy Minimization ; Title of run<br>cpp                = /lib/cpp         ; Preprocessor: Line tell the program the standard locations where to find certain files<br>
define                  = -DFLEXIBLE          ; defines to pass to the preprocessor<br><br>; Run Control<br>integrator            = steep        ; steep integrator (steep = steepest descent minimization)<br>nsteps                = 2500        ; maximum number of steps to integrate<br>
<br>; Energy Minimization<br>emtol                = 1000.0         ; [kJ/mol/nm] minimization is converged when max force is &lt; emtol<br>emstep                  = 0.01               ; [nm] initial step-size<br><br>; Output Control<br>
nstxout                 = 0             ; [steps] freq to write coordinates to trajectory<br>nstvout                 = 0             ; [steps] freq to write velocities to trajectory<br>nstfout                 = 0             ; [steps] freq to write forces to trajectory<br>
nstlog                  = 1             ; [steps] freq to write energies to log file<br>nstenergy            = 1        ; [steps] freq to write energies to energy file<br>energygrps            = System    ; group(s) to write to energy file<br>
<br>; Neighbor Searching Parameters<br>nstlist                 = 5                 ; [steps] freq to update neighbor list<br>ns-type                 = Grid              ; method of updating neighbor list<br>pbc                = xyz                ; periodic boundary conditions (yes/no)in all directions<br>
rlist                   = 0.9               ; [nm] cut-off distance for the short-range neighbor list<br><br>; Electrostatics<br>coulombtype             = Reaction-Field  ; Reaction-Field electrostatics<br>rcoulomb                = 1.4             ; [nm] distance for Coulomb cut-off<br>
epsilon_rf              = 54              ; The relative dielectric constant of the reaction field<br><br>; VdW<br>vdw-type                = Cut-off           ; twin-range cut-off with rlist where rvdw &gt;= rlist<br>rvdw                    = 1.4               ; [nm] distance for LJ cut-off<br>
<br>; Bonds<br>constraints             = none         ; convert all bonds to constraints<br clear="all"><br>-- <br>Ahmet Yıldırım<br><br>