Dear all,<br><br>I am trying to study the effect of pressure on
total potential of my system (8 polymer chains). My problem is that I dont see a systematic
effect of pressure on potentials and I cant judge if different pressures increase or decrease potential. This is the critical
observable in my system and with high fluctuations I am getting I cant
make comment on pressure effect. Total drift is high in most potential
functions..I start my runs from a frame which is the output of an older
NPT run (I use cpt file) that has a close density to what I want. In the production runs (NPT for 12 27 70 bar). <br><br>Below is the settings I
am using and I really appreciate it if you could comment on the most
important factors for such a study. I tried different cutoffs as
well...I though maybe increasing cutoffs invloves more interactions and
can represent better the pressure effect...<br>
<br>Thanks so much!<div class="im"><br> <br>; Run control <br>integrator = md <br>dt = 0.002 <br></div>nsteps = 1000000 ;5000 <br>
<div class="im">
nstcomm = 100 <br><br>; Output control<br>nstenergy = 100 <br>nstxout = 100 <br>nstvout = 0<br>nstfout = 0<br>
nstlog = 1000 <br>nstxtcout = 1000 <br><br>; Neighbor searching<br>nstlist = 10 <br>ns_type = grid <br><br>
; Electrostatics/VdW <br></div>coulombtype = Shift <br>vdw-type = Shift <br>rcoulomb-switch = 0.5 ;0 <br>rvdw-switch = 0.9 ;0 <br>
<br>; Cut-offs<br>rlist = 1.32 ;1.25 ; tired different cutoffs and r -switch...<br>rcoulomb = 1.1 ;1.0 <br>rvdw = 1.1 ;1.0 <br>
<div class="im"><br>; Temperature coupling <br>
Tcoupl = v-rescale <br>tc-grps = System <br>tau_t = 0.1 <br>ref_t = 300 <br> <br>; Pressure coupling<br>Pcoupl = Parrinello-Rahman <br>
Pcoupltype = isotropic <br></div>tau_p = 1 <br>compressibility = 3.5e-5 <br>ref_p = 10 <br><br>; Velocity generation <br>
gen_vel = no;yes <br>gen_temp = 300.0 <br>gen_seed = 173529 <br><br>; Bonds<div class="im"><br>constraints = all-bonds <br>
constraint-algorithm = lincs<br><br><br></div>results for 12 27 70 bar resp.<br><br><br><p class="MsoNormal"><span style="font-size: 9pt;">Statistics over 2043101 steps
[ 500.0000 through 4586.2000 ps ], 17 data sets</span></p>
<p class="MsoNormal"><span style="font-size: 9pt;">All statistics are over 204311
points</span></p><div class="im">
<p class="MsoNormal"><span style="font-size: 9pt;"> </span></p>
<p class="MsoNormal"><span style="font-size: 9pt;">Energy<span> </span>Average<span> </span>Err.Est.<span> </span>RMSD<span>
</span>Tot-Drift</span></p>
<p class="MsoNormal"><span style="font-size: 9pt;">-------------------------------------------------------------------------------</span></p>
</div><br><p class="MsoNormal"><span style="font-size: 9pt;">LJ (SR)<span> </span>-634.358<span> </span>2.9<span>
</span>11.0696<span> </span>-20.3551<span> </span>(kJ/mol)</span></p>
<p class="MsoNormal"><span style="font-size: 9pt;">Coulomb (SR)<span> </span>184.082<span> </span><span> </span>1.4<span>
</span>3.62712<span> </span>9.04046<span> </span>(kJ/mol)</span></p>
<p class="MsoNormal"><span style="font-size: 9pt;">P<b>otential<span> </span>642.528<span> </span>6.4<span>
</span>23.1897<span> </span>-44.6636<span> </span>(kJ/mol)</b></span></p>
<p class="MsoNormal"><span style="font-size: 9pt;">Kinetic En.<span> </span>904.294<span> </span>0.075<span>
</span>16.2742<span> </span>0.382223<span> </span>(kJ/mol)</span></p>
<p class="MsoNormal"><span style="font-size: 9pt;">Total Energy<span> </span>1546.82<span> </span>6.3<span>
</span>28.6865<span> </span>-44.2813<span> </span>(kJ/mol)</span></p>
<p class="MsoNormal"><span style="font-size: 9pt;">Temperature<span> </span>300.186<span> </span>0.025<span>
</span>5.4023<span> </span>0.126881<span> </span>(K)</span></p>
<p class="MsoNormal"><span style="font-size: 9pt;" lang="IT">Pressure<span> </span>12.3856<span> </span>0.89<span>
</span>887.501<span> </span>5.41599<span> </span>(bar)</span></p><p class="MsoNormal"><span style="font-size: 9pt;">Density<span> </span>824.417<span> </span>2.1<span>
</span>9.27838<span> </span>14.7965<span> </span>(kg/m^3)</span></p>
<p class="MsoNormal"><span style="font-size: 9pt;"> </span></p>
<p class="MsoNormal"><span style="font-size: 9pt;"><span> </span></span><span style="font-size: 9pt;"></span></p><p class="MsoNormal"><span style="font-size: 9pt;"><br></span></p>
<p class="MsoNormal"><span style="font-size: 9pt;"><br></span></p>
<p class="MsoNormal"><span style="font-size: 9pt;">Statistics over 750001 steps [
500.0000 through 2000.0000 ps ], 17 data sets</span></p>
<p class="MsoNormal"><span style="font-size: 9pt;">All statistics are over 75001
points</span></p><div class="im">
<p class="MsoNormal"><span style="font-size: 9pt;"> </span></p>
<p class="MsoNormal"><span style="font-size: 9pt;">Energy<span> </span>Average<span> </span>Err.Est.<span> </span>RMSD<span>
</span>Tot-Drift</span></p>
<p class="MsoNormal"><span style="font-size: 9pt;">-------------------------------------------------------------------------------</span></p>
</div><br><p class="MsoNormal"><span style="font-size: 9pt;">LJ (SR)<span> </span>-638.643<span> </span>4.3<span>
</span>12.0718<span> </span>-10.2094<span> </span>(kJ/mol)</span></p>
<p class="MsoNormal"><span style="font-size: 9pt;">Coulomb (SR)<span> </span>184.51<span> </span>1<span>
</span>2.89777<span> </span>5.99117<span> </span>(kJ/mol)</span></p>
<p class="MsoNormal"><b><span style="font-size: 9pt;">Potential<span> </span>634.902<span> </span><span> </span>5.7<span>
</span>22.2857<span> </span>-21.4761<span> </span>(kJ/mol)</span></b></p>
<p class="MsoNormal"><span style="font-size: 9pt;">Kinetic En.<span> </span>904.181<span> </span>0.11<span>
</span>16.2261<span> </span>-0.275076<span> </span>(kJ/mol)</span></p>
<p class="MsoNormal"><span style="font-size: 9pt;">Total Energy<span> </span>1539.08<span> </span>5.7<span>
</span>27.9661<span> </span>-21.7511<span> </span>(kJ/mol)</span></p>
<p class="MsoNormal"><span style="font-size: 9pt;">Temperature<span> </span>300.148<span> </span>0.035<span>
</span>5.38636 -0.0913135<span> </span>(K)</span></p>
<p class="MsoNormal"><span style="font-size: 9pt;" lang="IT">Pressure<span> </span>27.6467<span> </span>1.4<span>
</span>881.409<span> </span>8.58275<span> </span>(bar)</span></p><p class="MsoNormal"><span style="font-size: 9pt;">Density<span> </span>826.734<span> </span><span> </span>3.4<span>
</span>9.76089<span> </span>6.06824<span> </span>(kg/m^3)</span></p>
<p class="MsoNormal"><span style="font-size: 9pt;"> </span></p>
<p class="MsoNormal"><span style="font-size: 9pt;"> </span></p><p class="MsoNormal">70 bar run</p><p class="MsoNormal"><br><span style="font-size: 9pt;"></span></p><p class="MsoNormal">even 6 ns runs gives large total drifts..e.g.<span style="font-size: 9pt;"><span></span>13.4934 for density..</span> <br>
<span style="font-size: 9pt;"></span></p><p class="MsoNormal"><span style="font-size: 9pt;"></span></p><p class="MsoNormal"><br><span style="font-size: 9pt;"></span></p><p class="MsoNormal"><span style="font-size: 9pt;"><br>
</span></p>
<p class="MsoNormal"><span style="font-size: 9pt;">Statistics over 2750001 steps
[ 500.0000 through 6000.0000 ps ], 17 data sets</span></p>
<p class="MsoNormal"><span style="font-size: 9pt;">All statistics are over 275001
points</span></p><div class="im">
<p class="MsoNormal"><span style="font-size: 9pt;"> </span></p>
<p class="MsoNormal"><span style="font-size: 9pt;">Energy<span> </span>Average<span> </span>Err.Est.<span> </span>RMSD<span>
</span>Tot-Drift</span></p>
<p class="MsoNormal"><span style="font-size: 9pt;">-------------------------------------------------------------------------------</span></p>
</div><br><p class="MsoNormal"><span style="font-size: 9pt;">LJ (SR)<span> </span>-639.206<span> </span>3.7<span>
</span>11.6741<span> </span>-23.7773<span> </span>(kJ/mol)</span></p>
<p class="MsoNormal"><span style="font-size: 9pt;">Coulomb (SR)<span> </span>182.97<span> </span>1.7<span>
</span>4.18663<span> </span>11.8694<span> </span>(kJ/mol)</span></p>
<p class="MsoNormal"><b><span style="font-size: 9pt;">Potential<span> </span><span> </span>640.114<span> </span>7.5<span>
</span>24.9191<span> </span>-51.8187<span> </span>(kJ/mol)</span></b></p>
<p class="MsoNormal"><span style="font-size: 9pt;">Kinetic En.<span> </span>904.3<span> </span>0.074<span>
</span>16.2887<span> </span>0.161695<span> </span>(kJ/mol)</span></p>
<p class="MsoNormal"><span style="font-size: 9pt;">Total Energy<span> </span>1544.41<span> </span>7.5<span>
</span>30.1347<span> </span>-51.657<span> </span>(kJ/mol)</span></p>
<p class="MsoNormal"><span style="font-size: 9pt;">Temperature<span> </span>300.187<span> </span><span> </span>0.024<span>
</span>5.40713<span> </span>0.0536754<span> </span>(K)</span></p>
<p class="MsoNormal"><span style="font-size: 9pt;" lang="IT">Pressure<span> </span>69.7658<span> </span>0.86<span>
</span>893.933<span> </span>-2.29885<span> </span>(bar)</span></p><p class="MsoNormal"><span style="font-size: 9pt;">Density<span> </span><span> </span>829.657<span> </span>2.3<span>
</span>8.98849<span> </span>13.4934<span> </span>(kg/m^3)</span></p>