[gmx-users] LINC warning but reasonable potential energy and force

Moeed lecielll at googlemail.com
Tue Jul 20 16:34:15 CEST 2010


Dear experts,

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

***********************************************************************************************

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....

Please let me know if my results are reliable...

Thank you for your help :)
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