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<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">Hello Justin,</span></p><p class="MsoNormal"><br></p><p class="MsoNormal">[Actually, the reason I posted some parts of my mdp file was because you said I am sending redundant information so I just deleted the first lines of mdp file :) ]<br>
</p><p class="MsoNormal"><br><span style="font-size: 11pt; font-family: Arial;"></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">To get the xtc file initially I used nrexcl=3 in the top file. Then I used mdrun -rerun to breakdown energies on this xtc file with new top file </span><span style="font-size: 11pt; font-family: Arial;">nrexcl=7 to exclude all intramolecular nonbonded interactions (you definitely recall all these details :) <br>
</span></p><p class="MsoNormal"><br><span style="font-size: 11pt; font-family: Arial;"></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">1- Does it matter in the first run (to get xtc) what option I use for </span><span style="font-size: 11pt; font-family: Arial;">nrexcl in top file. Actually, I thought maybe in the normal run I have to set this option to zero. I did that and I got lincs warning (the same applies for </span><span style="font-size: 11pt; font-family: Arial;">nrexcl=1). So I tried </span><span style="font-size: 11pt; font-family: Arial;">nrexcl=2 and I noticed the results are not the same as nrexcl 3. However, this means I am still having nonbonded intramolecular interaction between atoms that are less than 2 bonds away. Am I right?<br>
</span></p><p class="MsoNormal"><br><span style="font-size: 11pt; font-family: Arial;"></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">2- I am wondering why in this breakdown I still see LJ and coloumb 1-4 interactions while I have </span><span style="font-size: 11pt; font-family: Arial;">nrexcl=2.</span></p>
<p class="MsoNormal"><br><span style="font-size: 11pt; font-family: Arial;"></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">3- In the second set of results (</span><span style="font-size: 11pt; font-family: Arial;">nrexcl=3) potential energy is 2766 > 2156 (the value for </span><span style="font-size: 11pt; font-family: Arial;">nrexcl==2). Logically, when 3 bonds away are excluded potential energy should be less I think!.. <br>
</span></p><p class="MsoNormal"><br><span style="font-size: 11pt; font-family: Arial;"></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">4- Regarding the units, in chapter 2 of manual the units for energy is in KJ/mol. Here is this table I see heat capacity is given in J/mol K. Could you please kindly tell me the units what is the unit for energy temrs LJ or coulomb?</span></p>
<p class="MsoNormal"><br><span style="font-size: 11pt; font-family: Arial;"></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">5- Very important question: If I want to compute the interaction energies BETWEEN molecuels, do I have to sum up LJ (SR) =(-3026 e.g) and coloumb (SR)=74 ? and can I conclude that there is a net attraction energy in the system?</span></p>
<p class="MsoNormal"><br><span style="font-size: 11pt; font-family: Arial;"></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">6- If I want to assure that equilibrium is reached, can I make the simulation time long enough such that T reaches 300 K? now it is 297 K.</span></p>
<p class="MsoNormal"><br><span style="font-size: 11pt; font-family: Arial;"></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">I appreciate your help.</span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">Thanks</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">Moeed<br></span></p><p class="MsoNormal"><br><span style="font-size: 11pt; font-family: Arial;"></span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"><br>
</span></p><p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p><p class="MsoNormal"><font size="2"><span style="font-family: Arial;"><u>mdrun
-rerun on trajectory for nrexcl=2 in top file</u></span></font></p><p class="MsoNormal"><br><font size="2"><span style="font-family: Arial;"></span></font></p>
<p class="MsoNormal"><font size="2"><span style="font-family: Arial;">Energy<span> </span>Average<span> </span>RMSD<span>
</span>Fluct.<span> </span>Drift<span> </span>Tot-Drift</span></font></p>
<p class="MsoNormal"><font size="2"><span style="font-family: Arial;"> </span></font></p>
<p class="MsoNormal"><font size="2"><span style="font-family: Arial;">-------------------------------------------------------------------------------</span></font></p>
<p class="MsoNormal"><font size="2"><span style="font-family: Arial;"> </span></font></p>
<p class="MsoNormal"><font size="2"><span style="font-family: Arial;">Angle<span> </span>4286.19<span> </span>258.765<span>
</span>231.378<span> </span>40.1269<span> </span>401.349</span></font></p>
<p class="MsoNormal"><font size="2"><span style="font-family: Arial;"> </span></font></p>
<p class="MsoNormal"><font size="2"><span style="font-family: Arial;">Ryckaert-Bell.<span> </span>722.966<span> </span>69.0616<span>
</span>61.1677<span> </span>11.1046<span> </span>111.068</span></font></p>
<p class="MsoNormal"><font size="2"><span style="font-family: Arial;"> </span></font></p>
<p class="MsoNormal"><font size="2"><b><span style="font-family: Arial;">LJ-14<span> </span><span> </span>498.432<span> </span>31.2891<span>
</span>30.9138<span> </span>1.67344<span> </span>16.7378</span></b></font></p>
<p class="MsoNormal"><font size="2"><b><span style="font-family: Arial;"> </span></b></font></p>
<p class="MsoNormal"><font size="2"><b><span style="font-family: Arial;">Coulomb-14<span> </span>-322.264<span> </span>11.5056<span>
</span>10.1507<span> </span>1.87612<span> </span>18.765</span></b></font></p>
<p class="MsoNormal"><font size="2"><b><span style="font-family: Arial;"> </span></b></font></p>
<p class="MsoNormal"><font size="2"><b><span style="font-family: Arial;">LJ
(SR)<span> </span>-3026.03<span> </span>45.5198<span>
</span>38.6106<span> </span>8.35011<span> </span>83.5178</span></b></font></p>
<p class="MsoNormal"><font size="2"><b><span style="font-family: Arial;"> </span></b></font></p>
<p class="MsoNormal"><font size="2"><span style="font-family: Arial;"><b>Coulomb
(SR)<span> </span>74.4564<span> </span>2.53605<span>
</span>2.53537<span> </span>0.02034<span> </span>0.203441</b></span></font></p>
<p class="MsoNormal"><font size="2"><span style="font-family: Arial;"> </span></font></p>
<p class="MsoNormal"><font size="2"><span style="font-family: Arial;">Coul.
recip.<span> </span>-77.5276<span> </span>2.3709<span>
</span>1.31777<span> </span>-0.682623<span> </span>-6.8276</span></font></p>
<p class="MsoNormal"><font size="2"><span style="font-family: Arial;"> </span></font></p>
<p class="MsoNormal"><font size="2"><span style="font-family: Arial;">Potential<span> </span>2156.22<span> </span>335.429<span>
</span>282.807<span> </span>62.4689<span> </span>624.814</span></font></p>
<p class="MsoNormal"><font size="2"><span style="font-family: Arial;"> </span></font></p>
<p class="MsoNormal"><font size="2"><span style="font-family: Arial;">Kinetic
En.<span> </span>0<span> </span>0<span> </span>0<span> </span>0<span> </span>0</span></font></p>
<p class="MsoNormal"><font size="2"><span style="font-family: Arial;"> </span></font></p>
<p class="MsoNormal"><font size="2"><span style="font-family: Arial;">Total
Energy<span> </span>2156.22<span> </span>335.429<span>
</span>282.807<span> </span>62.4689<span> </span>624.814</span></font></p>
<p class="MsoNormal"><font size="2"><span style="font-family: Arial;"> </span></font></p>
<p class="MsoNormal"><font size="2"><span style="font-family: Arial;">Temperature<span> </span>0<span> </span>0<span> </span>0<span> </span>0<span>
</span>0</span></font></p>
<p class="MsoNormal"><font size="2"><span style="font-family: Arial;"> </span></font></p>
<p class="MsoNormal"><font size="2"><span style="font-family: Arial;">Pressure
(bar)<span> </span>1563.28<span> </span>161.924<span>
</span>161.475 <span> </span>4.17097<span> </span>41.718</span></font></p>
<p class="MsoNormal"><font size="2"><span style="font-family: Arial;"> </span></font></p>
<p class="MsoNormal"><font size="2"><span style="font-family: Arial;">Cons. rmsd
()<span> </span>0<span> </span>0<span> </span>0<span> </span>0<span>
</span>0</span></font></p>
<p class="MsoNormal"><font size="2"><span style="font-family: Arial;"> </span></font></p>
<p class="MsoNormal"><font size="2"><span style="font-family: Arial;">Mu-X<span> </span>-0.00385475<span> </span>0.893851<span>
</span>0.893682 -0.00602335 -0.0602456</span></font></p>
<p class="MsoNormal"><font size="2"><span style="font-family: Arial;"> </span></font></p>
<p class="MsoNormal"><font size="2"><span style="font-family: Arial;">Heat
Capacity Cv:<span> </span>nan J/mol K (factor
= nan)</span></font></p><p class="MsoNormal"><font size="2"><br></font></p><p class="MsoNormal"><br></p><p class="MsoNormal"><br></p><p class="MsoNormal"><u><br></u></p><meta http-equiv="Content-Type" content="text/html; charset=utf-8"><meta name="ProgId" content="Word.Document"><meta name="Generator" content="Microsoft Word 11"><meta name="Originator" content="Microsoft Word 11"><link rel="File-List" href="file:///C:%5CDOCUME%7E1%5Cmoeed%5CLOCALS%7E1%5CTemp%5Cmsohtml1%5C01%5Cclip_filelist.xml"><style>
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<p class="MsoNormal"><u><span style="font-size: 11pt; font-family: Arial;">mdrun
-rerun on </span><span style="font-size: 11pt; font-family: Arial;">trajectory for nrexcl=3 in top file</span></u></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">Statistics
over 5001 steps [ 0.0000 thru 10.0000 ps ], 14 data sets</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">All
averages are over 501 frames</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"> </span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">Energy<span style=""> </span>Average<span style=""> </span>RMSD<span style="">
</span>Fluct.<span style=""> </span>Drift<span style=""> </span>Tot-Drift</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">-------------------------------------------------------------------------------</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">Angle<span style=""> </span>4400.09<span style=""> </span>284.259<span style="">
</span>237.268<span style=""> </span>54.2184<span style=""> </span>542.293</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">Ryckaert-Bell.<span style=""> </span>1009.62<span style=""> </span>124.468<span style="">
</span>94.0379<span style=""> </span>28.2417<span style=""> </span>282.474</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><b><span style="font-size: 11pt; font-family: Arial;">LJ-14<span style=""> </span>648.411<span style=""> </span>40.6844<span style="">
</span>39.926<span style=""> </span>2.70793<span style=""> </span>27.0848</span></b></p>
<p class="MsoNormal"><b><span style="font-size: 11pt; font-family: Arial;"></span></b></p>
<p class="MsoNormal"><b><span style="font-size: 11pt; font-family: Arial;">Coulomb-14<span style=""> </span>-278.654<span style=""> </span>34.4227<span style="">
</span>11.8071<span style=""> </span>11.1987<span style=""> </span>112.01</span></b></p>
<p class="MsoNormal"><b><span style="font-size: 11pt; font-family: Arial;"></span></b></p>
<p class="MsoNormal"><b><span style="font-size: 11pt; font-family: Arial;">LJ
(SR)<span style=""> </span>-3010.16<span style=""> </span>47.968<span style="">
</span>42.5388<span style=""> </span>7.67736<span style=""> </span>76.789</span></b></p>
<p class="MsoNormal"><b><span style="font-size: 11pt; font-family: Arial;"></span></b></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"><b>Coulomb
(SR)<span style=""> </span>74.7846<span style=""> </span>2.5186<span style="">
</span>2.47007<span style=""> </span>0.170417<span style=""> </span>1.70451</b></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">Coul.
recip.<span style=""> </span>-78.0436<span style=""> </span>2.58606<span style="">
</span>1.54725<span style=""> </span>-0.717662<span style=""> </span>-7.17805</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">Potential<span style=""> </span>2766.05<span style=""> </span>454.268<span style="">
</span>342.141<span style=""> </span>103.497<span style=""> </span>1035.18</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">Kinetic
En.<span style=""> </span>0<span style=""> </span>0<span style=""> </span>0<span style=""> </span>0<span style=""> </span>0</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">Total
Energy<span style=""> </span>2766.05<span style=""> </span>454.268<span style="">
</span>342.141<span style=""> </span>103.497<span style=""> </span>1035.18</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">Temperature<span style=""> </span>0<span style=""> </span>0<span style=""> </span>0<span style=""> </span>0<span style="">
</span>0</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">Pressure
(bar)<span style=""> </span>1973.01<span style=""> </span>177.068<span style="">
</span>172.803<span style=""> </span>13.3792<span style=""> </span>133.819</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">Cons. rmsd
()<span style=""> </span>0<span style=""> </span>0<span style=""> </span>0<span style=""> </span>0<span style="">
</span>0</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;">Mu-X<span style=""> </span>-0.0523974<span style=""> </span>0.826473<span style="">
</span>0.826318 -0.00553723 -0.0553834</span></p>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"></span></p>
<span style="font-size: 11pt; font-family: Arial;">Heat
Capacity Cv:<span style=""> </span>nan J/mol K (factor
= nan)<br><br><br><br><br>; Run control<br>integrator = md<br>dt = 0.002 ; ps !<br>nsteps = 5000 ; total 1.0 ps.<br>nstcomm = 1 ; frequency for center of mass motion removal <br>
<br>; Output control<br>nstenergy = 10 ; frequency to write energies to energy file. i.e., energies and other statistical data are stored every 10 steps<br>nstxout = 10 ; frequency to write coordinates/velocity/force to output trajectory file<br>
nstvout = 0<br>nstfout = 10<br>nstlog = 10 ; frequency to write energies to log file<br>nstxtcout = 10 <br><br>; Neighbor searching<br>nstlist = 10 ; neighborlist will be updated at least every 10 steps <br>
;ns_type = grid<br><br>; Electrostatics/VdW<br>coulombtype = PME <br>vdw-type = cut-off<br>; Cut-offs<br>rlist = 1.0<br>rcoulomb = 1.0<br>
rvdw = 1.0<br><br>; Temperature coupling Berendsen temperature coupling is on in two groups<br>Tcoupl = berendsen<br>tc-grps = HEX ;sol<br>tau_t = 0.1 ;0.1<br>
ref_t = 300 ;300<br><br>; Pressure coupling: Pressure coupling is not on<br>Pcoupl = no<br>tau_p = 0.5<br>compressibility = 4.5e-5<br>ref_p = 1.0<br>
<br>; Velocity generation Generate velocites is on at 300 K. Manual p155<br>gen_vel = yes<br>gen_temp = 300.0<br>gen_seed = 173529<br><br>; Bonds<br>constraints = all-bonds<br>
constraint-algorithm = lincs<br><br>pbc=xyz<br><br></span>
<p class="MsoNormal"><span style="font-size: 11pt; font-family: Arial;"> </span></p>
<p class="MsoNormal"><br></p><p class="MsoNormal"><br><span style="font-size: 11pt; font-family: Arial;"></span></p>
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