Dear experts,<br><br>I have been considering effect of fixing bond lengths in my system (constraints= none / all-bonds) on equilibrated density using NPT runs with 4.5.4. I am showing two set of results for two ref pressures of 10 and 70 bar. in case of constraints= none I had to employ a 0.5 fs timestep otherwise system blows up. Can you please comment why equilibrated densities are different for the same reference pressure? Thanks.<br>
<br>70 bar, all bonds constraint<br>timestep 2fs<br><br>Statistics over 875001 steps [ 250.0000 through 2000.0000 ps ], 2 data sets<br>All statistics are over 87501 points<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>Pressure 70.4993 0.092 542.944 0.222707 (bar)<br>Density 625.894 0.39 11.9075 0.110708 (kg/m^3)<br>
<br><br>70 bar, constraints= none<br>timestep 0.5 fs<br><br>Statistics over 3500001 steps [ 250.0000 through 2000.0000 ps ], 2 data sets<br>All statistics are over 350001 points<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>
-------------------------------------------------------------------------------<br>Pressure 70.6207 0.11 932.219 -0.500892 (bar)<br>Density 614.451 0.55 13.7381 -0.347349 (kg/m^3)<br>
<br><br>---<br><br>10 bar, all bonds constraint<br>
timestep 2fs<br><br>Statistics over 875001 steps [ 250.0000 through 2000.0000 ps ], 2 data sets<br>All statistics are over 87501 points<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>-------------------------------------------------------------------------------<br>
Pressure 10.4843 0.039 621.684 0.0156492 (bar)<br>Density 624.362 1 12.1354 -2.11725 (kg/m^3)<br><br><br>
10 bar, constraints= none<br>
timestep 0.5 fs<br><br>Statistics over 500001 steps [ 250.0000 through 500.0000 ps ], 2 data sets<br>All statistics are over 50001 points<br><br>Energy Average Err.Est. RMSD Tot-Drift<br>-------------------------------------------------------------------------------<br>
Temperature 299.92 0.11 4.86352 -0.139097 (K)<br>Density 600.689 2 14.7597 11.6485 (kg/m^3)<br><br><br>; Run control <br>integrator = md <br>
dt = 0.002 ; 0.0005 for constraints =none otherwise blows up <br>nsteps = 1000000 <br>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>coulombtype = shift <br>vdw-type = Shift <br>
rcoulomb-switch = 0 <br>rvdw-switch = 0.9 <br><br>; Cut-offs<br>rlist = 1.25 <br>rcoulomb = 1.0<br>rvdw = 1.0 <br>
<br><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>tau_p = 2 <br>compressibility = 4.5e-5 4.5e-5 <br>
ref_p = 10 <br><br>constraints = all-bonds <br>constraint-algorithm = lincs<br><br><div style="visibility: hidden; left: -5000px; position: absolute; z-index: 9999; padding: 0px; margin-left: 0px; margin-top: 0px; overflow: hidden; word-wrap: break-word; color: black; font-size: 10px; text-align: left; line-height: 130%;" id="avg_ls_inline_popup">
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