<font size="2"><span style="font-family: "Times New Roman";">Hello Justin,<br><br>The energy values I get differ mainly for LJ and coulomb(SR) terms. I read through chapter 4 of manual but I did not find the difference between LJ/coulomb 1-4 and SR. <br>
<br>1-Where can I read about the differences of these?<br>2-Do you think the difference in energies as a result of excluding intramolecualr nonbonded interactions are reasonable?<br>3-I can not figure out why pressure in the first case in negative and it is very large when exclusions are included.Also in the second case kinetic energy is zero. :(<br>
4-If I want to perform NPT simulation, the only thing I need to do is to switch on Pcoupl option in mdp file?<br><br>Thank you for your help.<br><br>No exclusions: mdrun -s Hexane-Stack125_md.tpr -o Hexane-Stack125_md.tpr<b>
<u>-x trajectoy.xtc</u> </b>-c Hexane-Stack125_after_md -v >&
output.mdrun_md<br><br>g_energy -f ener.edr -o energy.xvg:</span></font><font size="2"><br><span style="font-family: "Times New Roman";"><br>tatistics over 5001 steps [ 0.0000 thru 10.0000 ps ], 13 data sets<br>
The term 'Cons. rmsd ()' is averaged over 501 frames<br>All other averages are exact over 5001 steps<br><br>Energy Average RMSD Fluct. Drift Tot-Drift<br>-------------------------------------------------------------------------------<br>
Angle 4400.14 259.533 194.602 59.4737 594.856<br>Ryckaert-Bell. 1000.11 115.318 88.7683 25.494 254.991<br>LJ-14 648.7 37.6872 36.5595 3.16904 31.6967<br>
Coulomb-14 -281.387 32.3948 12.468 10.3554 103.574<br><b>LJ (SR) -3322.54 46.1011 40.9609 7.32669 73.2816<br>Coulomb (SR) 667.867 26.5968 9.4795 -8.60663 -86.0835</b><br>
Coul. recip. 921.791 26.6407 8.48573 -8.74618 -87.4793<br><b>Potential 4034.68 386.493 290.055 88.466 884.837</b><br>Kinetic En. 6336.76 250.507 237.567 27.5244 275.299<br>
Total Energy 10371.4 561.13 450.23 115.99 1160.14<br>Temperature 297.592 11.7645 11.1568 1.29262 12.9288<br>P<b>ressure (bar) -37.0417 1165.58 1161.54 -33.5839 -335.906</b><br>
Cons. rmsd () 3.74741e-06 2.92095e-07 2.34721e-07 6.02133e-08 6.02253e-07<br>Heat Capacity Cv: 12.5011 J/mol K (factor = 0.00156281)<br><br><br></span></font><font size="2"><span style="font-family: "Times New Roman";"></span></font>
<p class="MsoNormal" style="text-align: justify;"><font size="2">run with exclusions in top file: mdrun -<b>rerun trajectoy.xtc</b> -s
Hexane-Stack125_md.tpr -o Hexane-Stack125_md.tpr -c Hexane-Stack125_after_md -v
>& output.mdrun_md</font></p><p class="MsoNormal" style="text-align: justify;">Statistics over 5001 steps [ 0.0000 thru 10.0000 ps ], 13 data sets<br>All averages are over 501 frames<br><br>Energy Average RMSD Fluct. Drift Tot-Drift<br>
-------------------------------------------------------------------------------<br>Angle 4400.09 284.259 237.268 54.2184 542.293<br>Ryckaert-Bell. 1009.62 124.468 94.0379 28.2417 282.474<br>
LJ-14 648.411 40.6844 39.926 2.70793 27.0848<br>Coulomb-14 -278.654 34.4227 11.8071 11.1987 112.01<br><b>LJ (SR) -3010.16 47.968 42.5388 7.67736 76.789<br>
Coulomb (SR) 74.7846 2.5186 2.47007 0.170417 1.70451</b><br>Coul. recip. -78.0436 2.58606 1.54725 -0.717662 -7.17805<br>Potential 2766.05 454.268 342.141 103.497 1035.18<br>
Kinetic En. 0 0 0 0 0<br>Total Energy 2766.05 454.268 342.141 103.497 1035.18<br><b>Temperature 0 0 0 0 0<br>
Pressure (bar) 1973.01 177.068 172.803 13.3792 133.819</b><br>Cons. rmsd () 0 0 0 0 0<br>Heat Capacity Cv: nan J/mol K (factor = nan)<br>
<br></p><p class="MsoNormal" style="text-align: justify;"><font size="2">with: mdp file</font></p><p class="MsoNormal" style="text-align: justify;"><font size="2"> 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></font></p><br><font size="2"><span style="font-family: "Times New Roman";"><br></span></font><input type="hidden"><input type="hidden"><div></div>
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