Dear Dr. Chaban,
Thanks for you answer. Actually, I meant I have a .. system :). If you
remember I was trying to compress my system (PE only) to attain the density
I want. I worked on that problem for nearly one week and I posted the
procedure I used to reach what I want. Unfortunately, no one got back to me
on that problem, I wanted to know if you can help me please.
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...
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.
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.
:
Steepest Descents:
Tolerance (Fmax) = 1.00000e+03
Number of steps = 400
Step= 0, Dmax= 1.0e-02 nm, Epot= 1.32635e+08 Fmax= 2.29301e+10, atom=
1004
Step= 1, Dmax= 1.0e-02 nm, Epot= 2.22267e+07 Fmax= 1.39980e+09, atom=
1766
Step= 2, Dmax= 1.2e-02 nm, Epot= 8.21648e+06 Fmax= 2.00629e+08, atom=
968
Step= 3, Dmax= 1.4e-02 nm, Epot= 1.67342e+06 Fmax= 2.38551e+07, atom=
968
Step= 4, Dmax= 1.7e-02 nm, Epot= 4.59581e+05 Fmax= 3.28726e+06, atom=
121
Step= 5, Dmax= 2.1e-02 nm, Epot= 1.51948e+05 Fmax= 4.17261e+05, atom=
1766
Step= 6, Dmax= 2.5e-02 nm, Epot= 4.95460e+04 Fmax= 1.64740e+05, atom=
121
Step= 7, Dmax= 3.0e-02 nm, Epot= 3.20548e+04 Fmax= 8.22273e+04, atom=
968
Step= 8, Dmax= 3.6e-02 nm, Epot= 2.16962e+04 Fmax= 1.86463e+04, atom=
961
Step= 9, Dmax= 4.3e-02 nm, Epot= 1.29190e+04 Fmax= 3.92749e+03, atom=
1766
Step 10, time 0.02 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001238, max 0.029289 (between atoms 113 and 115)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
113 114 33.6 0.1090 0.1103 0.1090
1765 1766 36.2 0.1090 0.1075 0.1090
Step= 10, Dmax= 5.2e-02 nm, Epot= 8.04986e+03 Fmax= 3.49262e+04, atom=
826
Step 11, time 0.022 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000239, max 0.008502 (between atoms 1765 and 1767)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
825 826 32.2 0.1089 0.1096 0.1090
1765 1766 32.2 0.1075 0.1091 0.1090
Step= 11, Dmax= 6.2e-02 nm, Epot= 6.61167e+03 Fmax= 6.62618e+03, atom=
1766
Step 12, time 0.024 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000731, max 0.014345 (between atoms 1762 and 1765)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
825 826 31.4 0.1096 0.1081 0.1090
1765 1766 39.6 0.1091 0.1076 0.1090
Step= 12, Dmax= 7.4e-02 nm, Epot= 5.16869e+03 Fmax= 9.34606e+03, atom=
1766
Step 13, time 0.026 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000966, max 0.021083 (between atoms 1765 and 1767)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
825 826 46.4 0.1081 0.1107 0.1090
1765 1766 51.8 0.1076 0.1087 0.1090
Step= 13, Dmax= 8.9e-02 nm, Epot= 4.67001e+03 Fmax= 1.02723e+04, atom=
1766
Step 14, time 0.028 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.001976, max 0.050316 (between atoms 1765 and 1767)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
825 826 43.8 0.1107 0.1085 0.1090
1765 1766 92.7 0.1087 0.1128 0.1090
Step= 14, Dmax= 1.1e-01 nm, Epot= 4.40657e+03 Fmax= 4.61388e+03, atom=
826
Step 15, time 0.03 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.042648, max 1.350503 (between atoms 825 and 826)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
122 124 38.1 0.1093 0.1174 0.1090
122 123 34.0 0.1092 0.1165 0.1090
119 121 41.9 0.1092 0.1253 0.1090
119 120 44.7 0.1091 0.1219 0.1090
116 119 33.7 0.1541 0.1512 0.1529
113 116 40.5 0.1540 0.1564 0.1529
113 115 55.8 0.1095 0.1294 0.1090
113 114 49.4 0.1093 0.1263 0.1090
110 112 50.6 0.1094 0.1209 0.1090
110 111 53.4 0.1094 0.1218 0.1090
107 110 39.4 0.1534 0.1666 0.1529
107 108 35.4 0.1090 0.1178 0.1090
966 969 33.5 0.1534 0.1669 0.1529
966 968 44.8 0.1090 0.1172 0.1090
966 967 66.8 0.1091 0.1221 0.1090
963 965 38.5 0.1091 0.1181 0.1090
963 964 37.1 0.1091 0.1179 0.1090
831 834 31.6 0.1538 0.1448 0.1529
831 833 37.3 0.1099 0.0977 0.1090
828 831 55.2 0.1553 0.1785 0.1529
828 829 84.4 0.1113 0.1348 0.1090
825 828 56.5 0.1555 0.2214 0.1529
825 827 89.3 0.1102 0.1823 0.1090
825 826 89.2 0.1085 0.2562 0.1090
822 824 65.3 0.1092 0.1602 0.1090
822 823 51.3 0.1092 0.1482 0.1090
819 822 44.6 0.1534 0.1902 0.1529
1768 1770 45.1 0.1107 0.1528 0.1090
1768 1769 38.5 0.1101 0.1401 0.1090
1765 1768 55.7 0.1510 0.1687 0.1529
1765 1767 88.7 0.1145 0.1453 0.1090
1765 1766 90.4 0.1128 0.1744 0.1090
1762 1765 36.3 0.1601 0.1635 0.1529
1762 1764 42.7 0.1120 0.1163 0.1090
1762 1763 48.8 0.1101 0.1144 0.1090
1759 1760 38.9 0.1102 0.1097 0.1090
1591 1594 33.0 0.1533 0.1547 0.1529
1591 1593 36.9 0.1092 0.1158 0.1090
1591 1592 36.1 0.1091 0.1153 0.1090
1588 1590 38.0 0.1092 0.1140 0.1090
1588 1589 39.0 0.1092 0.1141 0.1090
1519 1522 34.1 0.1532 0.1709 0.1529
1519 1521 32.5 0.1091 0.1221 0.1090
1519 1520 35.2 0.1091 0.1232 0.1090
1516 1519 38.5 0.1533 0.1791 0.1529
1516 1518 51.8 0.1093 0.1334 0.1090
1516 1517 56.4 0.1094 0.1351 0.1090
1513 1515 58.5 0.1092 0.1557 0.1090
1513 1514 56.9 0.1092 0.1569 0.1090
1510 1513 60.5 0.1545 0.1522 0.1529
1510 1512 53.6 0.1103 0.1148 0.1090
1510 1511 41.7 0.1101 0.1016 0.1090
1507 1510 55.0 0.1545 0.1515 0.1529
1507 1509 58.9 0.1093 0.1563 0.1090
1507 1508 54.7 0.1092 0.1557 0.1090
1504 1506 45.3 0.1093 0.1293 0.1090
1504 1505 49.1 0.1094 0.1310 0.1090
1501 1504 38.9 0.1533 0.1749 0.1529
1818 1820 34.4 0.1091 0.1088 0.1090
2563 2565 39.8 0.1093 0.1167 0.1090
2563 2564 37.6 0.1093 0.1163 0.1090
2560 2562 42.1 0.1092 0.1220 0.1090
2560 2561 40.0 0.1092 0.1214 0.1090
2557 2560 35.8 0.1536 0.1535 0.1529
2554 2557 33.7 0.1537 0.1525 0.1529
2554 2556 37.1 0.1092 0.1219 0.1090
2554 2555 40.0 0.1092 0.1226 0.1090
2551 2553 36.5 0.1093 0.1167 0.1090
2551 2552 52.9 0.1092 0.1149 0.1090
Wrote pdb files with previous and current coordinates
Step= 15, Dmax= 1.3e-01 nm, Epot= 4.73137e+04 Fmax= 1.84271e+06, atom=
822
Step 16, time 0.032 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.005654, max 0.128942 (between atoms 825 and 828)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
828 829 30.8 0.1113 0.1110 0.1090
825 828 31.7 0.1555 0.1726 0.1529
825 827 47.4 0.1102 0.1221 0.1090
825 826 76.4 0.1085 0.1166 0.1090
822 824 34.7 0.1092 0.1223 0.1090
1765 1767 37.2 0.1145 0.1126 0.1090
1765 1766 47.4 0.1128 0.1127 0.1090
Step= 17, Dmax= 3.2e-02 nm, Epot= 3.09838e+03 Fmax= 2.83061e+03, atom=
1766
Step= 18, Dmax= 3.9e-02 nm, Epot= 2.91458e+03 Fmax= 2.84186e+03, atom=
828
Step 19, time 0.038 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.003357, max 0.050861 (between atoms 825 and 826)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
828 830 39.1 0.1095 0.1118 0.1090
825 826 39.2 0.1087 0.1145 0.1090
1516 1517 31.3 0.1094 0.1133 0.1090
Step= 20, Dmax= 2.3e-02 nm, Epot= 2.38983e+03 Fmax= 1.82748e+03, atom=
1516
Step= 22, Dmax= 1.4e-02 nm, Epot= 2.05520e+03 Fmax= 1.32025e+03, atom=
1510
Step= 23, Dmax= 1.7e-02 nm, Epot= 2.00275e+03 Fmax= 2.13164e+03, atom=
1516
Step= 24, Dmax= 2.0e-02 nm, Epot= 1.86550e+03 Fmax= 2.34225e+03, atom=
1510
Step= 25, Dmax= 2.4e-02 nm, Epot= 1.83379e+03 Fmax= 2.62066e+03, atom=
1519
Step= 27, Dmax= 1.4e-02 nm, Epot= 1.41757e+03 Fmax= 5.65049e+02, atom=
1513
writing lowest energy coordinates.
Steepest Descents converged to Fmax < 1000 in 28 steps
Potential Energy = 1.41757054835921e+03
Maximum force = 5.65049499838719e+02 on atom 1513
Norm of force = 7.42266925121288e+01
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