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 "Temperature=312.646"
(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 < 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 >= 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 Yýldýrým<br><br>