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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