[gmx-users] Simulation runs on iMac but explodes on cluster

[Luke Goodsell]

Hi Mark,

Perhaps your simulation is intrinsically unstable, and you haven't gotten
> unlucky enough yet on the iMac. Check out http://www.gromacs.org/**
> Documentation/Terminology/**Blowing_Up<http://www.gromacs.org/Documentation/Terminology/Blowing_Up>
>

The simulation on the iMac reaches a stable equilibrium. On the cluster, it
appears stable until step 14555 where I get LINCS warnings such as

 Step 14555, time 29.11 (ps)  LINCS WARNING
>
> relative constraint deviation after LINCS:
>
> rms 0.078151, max 2.416183 (between atoms 1720 and 1721)
>
> bonds that rotated more than 30 degrees:
>
>  atom 1 atom 2  angle  previous, current, constraint length
>
>    1720   1721  151.3    0.1080   0.3689      0.1080
>
>    1707   1708  152.8    0.1090   0.3674      0.1090
>
> Wrote pdb files with previous and current coordinates
>
>
>> Step 14555, time 29.11 (ps)  LINCS WARNING
>
> relative constraint deviation after LINCS:
>
> rms 0.078245, max 2.420384 (between atoms 1720 and 1721)
>
> bonds that rotated more than 30 degrees:
>
>  atom 1 atom 2  angle  previous, current, constraint length
>
>    1720   1721  151.3    0.1080   0.3694      0.1080
>
>    1707   1708  152.8    0.1090   0.3676      0.1090
>
>
>> Back Off! I just backed up step14555b.pdb to ./#step14555b.pdb.1#
>
>
>> Back Off! I just backed up step14555c.pdb to ./#step14555c.pdb.1#
>
> Wrote pdb files with previous and current coordinates
>
>
>> Step 14556, time 29.112 (ps)  LINCS WARNING
>
> relative constraint deviation after LINCS:
>
> rms 133.212808, max 5757.494141 (between atoms 1720 and 1721)
>
> bonds that rotated more than 30 degrees:
>
>  atom 1 atom 2  angle  previous, current, constraint length
>
>    1722   1724   36.7    0.1336   0.1716      0.1335
>
>    1722   1723   35.5    0.1230   0.1553      0.1229
>
>    1720   1721   90.0    0.3694 621.9174      0.1080
>
>    1718   1720  144.9    0.1407   0.5335      0.1400
>
>    1718   1719  105.6    0.1085   1.0804      0.1080
>
>    1716   1717   90.6    0.0960  24.8478      0.0960
>
>    1715   1718  136.5    0.1414   0.4281      0.1409
>
>    1715   1716   90.6    0.1366  37.5311      0.1364
>
>    1713   1715  111.6    0.1412   1.0479      0.1409
>
>    1713   1714  120.7    0.1082   0.3603      0.1080
>
>    1711   1713  118.7    0.1402   0.3129      0.1400
>
>    1711   1712   53.9    0.1082   0.1451      0.1080
>
>    1710   1720  101.0    0.1407   1.7692      0.1400
>
>    1710   1711   57.8    0.1404   0.2418      0.1400
>
>    1707   1710  112.0    0.1520   0.5543      0.1510
>
>    1707   1709  107.4    0.1098   0.5075      0.1090
>
>    1707   1708  102.7    0.3676   1.4700      0.1090
>
>    1705   1722   75.1    0.1525   0.2535      0.1522
>
>    1705   1707  106.7    0.1533   0.6142      0.1526
>
>    1705   1706   56.4    0.1093   0.1136      0.1090
>
>    1703   1705   89.0    0.1452   0.2683      0.1449
>
>    1703   1704   42.3    0.1010   0.1384      0.1010
>
>    1701   1703   38.9    0.1336   0.1768      0.1335
>
>    1673   1674   35.7    0.1229   0.1230      0.1229
>
>    1670   1673   31.2    0.1522   0.1523      0.1522
>
> Wrote pdb files with previous and current coordinates
>
>
>> Step 14556, time 29.112 (ps)  LINCS WARNING
>
> relative constraint deviation after LINCS:
>
> rms 133.228686, max 5758.184082 (between atoms 1720 and 1721)
>
> bonds that rotated more than 30 degrees:
>
>  atom 1 atom 2  angle  previous, current, constraint length
>
>    1722   1724   47.6    0.1336   0.1995      0.1335
>
>    1722   1723   45.8    0.1230   0.1781      0.1229
>
>    1720   1721   90.0    0.3694 621.9919      0.1080
>
>    1718   1720  141.7    0.1407   0.5243      0.1400
>
>    1718   1719  106.2    0.1085   1.1444      0.1080
>
>    1716   1717   90.7    0.0960  24.8269      0.0960
>
>    1715   1718  144.6    0.1414   0.5103      0.1409
>
>    1715   1716   90.6    0.1366  37.5424      0.1364
>
>    1713   1715  112.9    0.1412   1.0642      0.1409
>
>    1713   1714  120.9    0.1082   0.3765      0.1080
>
>    1711   1713  124.0    0.1402   0.2954      0.1400
>
>    1711   1712   52.5    0.1082   0.1399      0.1080
>
>    1710   1720  103.1    0.1407   1.8233      0.1400
>
>    1710   1711   75.5    0.1404   0.2584      0.1400
>
>    1707   1710  117.5    0.1520   0.6407      0.1510
>
>    1707   1709  109.9    0.1098   0.6153      0.1090
>
>    1707   1708  102.2    0.3676   1.5528      0.1090
>
>    1705   1722   92.4    0.1525   0.2917      0.1522
>
>    1705   1707  107.2    0.1533   0.7484      0.1526
>
>    1705   1706   57.0    0.1093   0.0958      0.1090
>
>    1703   1705   94.4    0.1452   0.3185      0.1449
>
>    1703   1704   49.7    0.1010   0.1528      0.1010
>
>    1701   1703   46.6    0.1336   0.1937      0.1335
>
>    1673   1674   35.7    0.1229   0.1230      0.1229
>
>    1670   1673   31.2    0.1522   0.1523      0.1522
>
>
>> Back Off! I just backed up step14556b.pdb to ./#step14556b.pdb.1#
>
>
>> Back Off! I just backed up step14556c.pdb to ./#step14556c.pdb.1#
>
> Wrote pdb files with previous and current coordinates
>
>
The system is 'blowing up', no (rms ~575.8nm between 1720 and 1721)?

It appears to me that there is some significant difference in the operation
of gromacs in the two environments.

Thanks,
Luke
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20110713/cd38c1a3/attachment.html>