[gmx-users] Re: Lincs warning but reasonable energy
Vitaly Chaban
vvchaban at gmail.com
Fri Jul 23 17:30:30 CEST 2010
Dear Moeed:
It seems to me that you are using not the best force field of the
polymer. Why do you apply constaints (LINCS warnings...)? As for the
compression degree and warnings, one cannot say anything sane about
your system without looking at the concrete molecular patterns and
probably dynamics.
If you are interested, send me all files of your system and I'll try
to look at them as a whole on the weekend.
Dr. Vitaly Chaban
> 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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