Dear experts,<br><br>I am trying to build up a polymer system. To do so I took a chain with 60 repeating units (ethylene) and compressed the system to attain the desired box volume (density). I took the following approach since after one week work on this problem I believe that is the only way of achieving what I want so I would like you to correct me if necessary. I know it might be a naive procedure... <br>
<br>I noticed that in either NPT or NVT trials for a long chain equilibrium state corresponds to more extended conformations. My problem is that with this conformation I can not compress the system enough as simulation crashes (when chain takes a extended conformation that is about 2 or 3 times longer than box size applying high pressure to reduce volume causes system to explode). Hence, after performing nearly 40 NPT and NVT (and combination of these) runs I came to the point that the only way to approach the volume I am after is forget the equilibrium state (as if simulation is long chain tens to extend) and look for the globule-like structure so the volume it occupies is minimal. For instance I did a NPT for 500ps and noticed at 130 ps molecule has the convoluted structure so in the next trial I picked simul. time of 130 ps to capture the structure I want, used editconf to reduce the size, energy minimized the structure and performed the next NPT with this initial structure. Doing so, I could approach the box size of 2.3 nm (desired size is 1.8nm). Since it was not possible to compress the system further I replicated this molecule and energy minimized the replicated system. Energy minimization gives reasonable force but potential is about 3000. I dont know if this is reasonable for such a packed system.<br>
<br>Then employed NPT to compress again to a volume a bit smaller than what I need and used editconf to attain the exact density I am after. Below is the output file of EM of the replicated and compressed system: I am getting some LINC warnings but at the end force and potential energies seem to be OK. PLease let me know if anything is going wrong.<br>
:<br>Steepest Descents:<br> Tolerance (Fmax) = 1.00000e+03<br> Number of steps = 400<br>Step= 0, Dmax= 1.0e-02 nm, Epot= 1.32635e+08 Fmax= 2.29301e+10, atom= 1004<br>Step= 1, Dmax= 1.0e-02 nm, Epot= 2.22267e+07 Fmax= 1.39980e+09, atom= 1766<br>
Step= 2, Dmax= 1.2e-02 nm, Epot= 8.21648e+06 Fmax= 2.00629e+08, atom= 968<br>Step= 3, Dmax= 1.4e-02 nm, Epot= 1.67342e+06 Fmax= 2.38551e+07, atom= 968<br>Step= 4, Dmax= 1.7e-02 nm, Epot= 4.59581e+05 Fmax= 3.28726e+06, atom= 121<br>
Step= 5, Dmax= 2.1e-02 nm, Epot= 1.51948e+05 Fmax= 4.17261e+05, atom= 1766<br>Step= 6, Dmax= 2.5e-02 nm, Epot= 4.95460e+04 Fmax= 1.64740e+05, atom= 121<br>Step= 7, Dmax= 3.0e-02 nm, Epot= 3.20548e+04 Fmax= 8.22273e+04, atom= 968<br>
Step= 8, Dmax= 3.6e-02 nm, Epot= 2.16962e+04 Fmax= 1.86463e+04, atom= 961<br>Step= 9, Dmax= 4.3e-02 nm, Epot= 1.29190e+04 Fmax= 3.92749e+03, atom= 1766<br><br>Step 10, time 0.02 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>
rms 0.001238, max 0.029289 (between atoms 113 and 115)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 113 114 33.6 0.1090 0.1103 0.1090<br>
1765 1766 36.2 0.1090 0.1075 0.1090<br>Step= 10, Dmax= 5.2e-02 nm, Epot= 8.04986e+03 Fmax= 3.49262e+04, atom= 826<br><br>Step 11, time 0.022 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>
rms 0.000239, max 0.008502 (between atoms 1765 and 1767)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 825 826 32.2 0.1089 0.1096 0.1090<br>
1765 1766 32.2 0.1075 0.1091 0.1090<br>Step= 11, Dmax= 6.2e-02 nm, Epot= 6.61167e+03 Fmax= 6.62618e+03, atom= 1766<br><br>Step 12, time 0.024 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>
rms 0.000731, max 0.014345 (between atoms 1762 and 1765)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 825 826 31.4 0.1096 0.1081 0.1090<br>
1765 1766 39.6 0.1091 0.1076 0.1090<br>Step= 12, Dmax= 7.4e-02 nm, Epot= 5.16869e+03 Fmax= 9.34606e+03, atom= 1766<br><br>Step 13, time 0.026 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>
rms 0.000966, max 0.021083 (between atoms 1765 and 1767)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 825 826 46.4 0.1081 0.1107 0.1090<br>
1765 1766 51.8 0.1076 0.1087 0.1090<br>Step= 13, Dmax= 8.9e-02 nm, Epot= 4.67001e+03 Fmax= 1.02723e+04, atom= 1766<br><br>Step 14, time 0.028 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>
rms 0.001976, max 0.050316 (between atoms 1765 and 1767)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 825 826 43.8 0.1107 0.1085 0.1090<br>
1765 1766 92.7 0.1087 0.1128 0.1090<br>Step= 14, Dmax= 1.1e-01 nm, Epot= 4.40657e+03 Fmax= 4.61388e+03, atom= 826<br><br>Step 15, time 0.03 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>
rms 0.042648, max 1.350503 (between atoms 825 and 826)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 122 124 38.1 0.1093 0.1174 0.1090<br>
122 123 34.0 0.1092 0.1165 0.1090<br> 119 121 41.9 0.1092 0.1253 0.1090<br> 119 120 44.7 0.1091 0.1219 0.1090<br> 116 119 33.7 0.1541 0.1512 0.1529<br>
113 116 40.5 0.1540 0.1564 0.1529<br> 113 115 55.8 0.1095 0.1294 0.1090<br> 113 114 49.4 0.1093 0.1263 0.1090<br> 110 112 50.6 0.1094 0.1209 0.1090<br>
110 111 53.4 0.1094 0.1218 0.1090<br> 107 110 39.4 0.1534 0.1666 0.1529<br> 107 108 35.4 0.1090 0.1178 0.1090<br> 966 969 33.5 0.1534 0.1669 0.1529<br>
966 968 44.8 0.1090 0.1172 0.1090<br> 966 967 66.8 0.1091 0.1221 0.1090<br> 963 965 38.5 0.1091 0.1181 0.1090<br> 963 964 37.1 0.1091 0.1179 0.1090<br>
831 834 31.6 0.1538 0.1448 0.1529<br> 831 833 37.3 0.1099 0.0977 0.1090<br> 828 831 55.2 0.1553 0.1785 0.1529<br> 828 829 84.4 0.1113 0.1348 0.1090<br>
825 828 56.5 0.1555 0.2214 0.1529<br> 825 827 89.3 0.1102 0.1823 0.1090<br> 825 826 89.2 0.1085 0.2562 0.1090<br> 822 824 65.3 0.1092 0.1602 0.1090<br>
822 823 51.3 0.1092 0.1482 0.1090<br> 819 822 44.6 0.1534 0.1902 0.1529<br> 1768 1770 45.1 0.1107 0.1528 0.1090<br> 1768 1769 38.5 0.1101 0.1401 0.1090<br>
1765 1768 55.7 0.1510 0.1687 0.1529<br> 1765 1767 88.7 0.1145 0.1453 0.1090<br> 1765 1766 90.4 0.1128 0.1744 0.1090<br> 1762 1765 36.3 0.1601 0.1635 0.1529<br>
1762 1764 42.7 0.1120 0.1163 0.1090<br> 1762 1763 48.8 0.1101 0.1144 0.1090<br> 1759 1760 38.9 0.1102 0.1097 0.1090<br> 1591 1594 33.0 0.1533 0.1547 0.1529<br>
1591 1593 36.9 0.1092 0.1158 0.1090<br> 1591 1592 36.1 0.1091 0.1153 0.1090<br> 1588 1590 38.0 0.1092 0.1140 0.1090<br> 1588 1589 39.0 0.1092 0.1141 0.1090<br>
1519 1522 34.1 0.1532 0.1709 0.1529<br> 1519 1521 32.5 0.1091 0.1221 0.1090<br> 1519 1520 35.2 0.1091 0.1232 0.1090<br> 1516 1519 38.5 0.1533 0.1791 0.1529<br>
1516 1518 51.8 0.1093 0.1334 0.1090<br> 1516 1517 56.4 0.1094 0.1351 0.1090<br> 1513 1515 58.5 0.1092 0.1557 0.1090<br> 1513 1514 56.9 0.1092 0.1569 0.1090<br>
1510 1513 60.5 0.1545 0.1522 0.1529<br> 1510 1512 53.6 0.1103 0.1148 0.1090<br> 1510 1511 41.7 0.1101 0.1016 0.1090<br> 1507 1510 55.0 0.1545 0.1515 0.1529<br>
1507 1509 58.9 0.1093 0.1563 0.1090<br> 1507 1508 54.7 0.1092 0.1557 0.1090<br> 1504 1506 45.3 0.1093 0.1293 0.1090<br> 1504 1505 49.1 0.1094 0.1310 0.1090<br>
1501 1504 38.9 0.1533 0.1749 0.1529<br> 1818 1820 34.4 0.1091 0.1088 0.1090<br> 2563 2565 39.8 0.1093 0.1167 0.1090<br> 2563 2564 37.6 0.1093 0.1163 0.1090<br>
2560 2562 42.1 0.1092 0.1220 0.1090<br> 2560 2561 40.0 0.1092 0.1214 0.1090<br> 2557 2560 35.8 0.1536 0.1535 0.1529<br> 2554 2557 33.7 0.1537 0.1525 0.1529<br>
2554 2556 37.1 0.1092 0.1219 0.1090<br> 2554 2555 40.0 0.1092 0.1226 0.1090<br> 2551 2553 36.5 0.1093 0.1167 0.1090<br> 2551 2552 52.9 0.1092 0.1149 0.1090<br>
Wrote pdb files with previous and current coordinates<br>Step= 15, Dmax= 1.3e-01 nm, Epot= 4.73137e+04 Fmax= 1.84271e+06, atom= 822<br>Step 16, time 0.032 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>
rms 0.005654, max 0.128942 (between atoms 825 and 828)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br> 828 829 30.8 0.1113 0.1110 0.1090<br>
825 828 31.7 0.1555 0.1726 0.1529<br> 825 827 47.4 0.1102 0.1221 0.1090<br> 825 826 76.4 0.1085 0.1166 0.1090<br> 822 824 34.7 0.1092 0.1223 0.1090<br>
1765 1767 37.2 0.1145 0.1126 0.1090<br> 1765 1766 47.4 0.1128 0.1127 0.1090<br>Step= 17, Dmax= 3.2e-02 nm, Epot= 3.09838e+03 Fmax= 2.83061e+03, atom= 1766<br>Step= 18, Dmax= 3.9e-02 nm, Epot= 2.91458e+03 Fmax= 2.84186e+03, atom= 828<br>
<br>Step 19, time 0.038 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 0.003357, max 0.050861 (between atoms 825 and 826)<br>bonds that rotated more than 30 degrees:<br> atom 1 atom 2 angle previous, current, constraint length<br>
828 830 39.1 0.1095 0.1118 0.1090<br> 825 826 39.2 0.1087 0.1145 0.1090<br> 1516 1517 31.3 0.1094 0.1133 0.1090<br>Step= 20, Dmax= 2.3e-02 nm, Epot= 2.38983e+03 Fmax= 1.82748e+03, atom= 1516<br>
Step= 22, Dmax= 1.4e-02 nm, Epot= 2.05520e+03 Fmax= 1.32025e+03, atom= 1510<br>Step= 23, Dmax= 1.7e-02 nm, Epot= 2.00275e+03 Fmax= 2.13164e+03, atom= 1516<br>Step= 24, Dmax= 2.0e-02 nm, Epot= 1.86550e+03 Fmax= 2.34225e+03, atom= 1510<br>
Step= 25, Dmax= 2.4e-02 nm, Epot= 1.83379e+03 Fmax= 2.62066e+03, atom= 1519<br>Step= 27, Dmax= 1.4e-02 nm, Epot= 1.41757e+03 Fmax= 5.65049e+02, atom= 1513<br><br>writing lowest energy coordinates.<br><br>Steepest Descents converged to Fmax < 1000 in 28 steps<br>
Potential Energy = 1.41757054835921e+03<br>Maximum force = 5.65049499838719e+02 on atom 1513<br>Norm of force = 7.42266925121288e+01<br><br>***********************************************************************************************<br>
<br>I tried a NVT for 500 ps and noticed PE LJ SR are reaching equilibrium (plateau after about 100ps). T coupling is working perfectly as well....<br><br>Please let me know if my results are reliable...<br><br>Thank you for your help :)<br>
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