On 13/07/2011 7:01 PM, Luke Goodsell wrote:
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
The simulation on the iMac reaches a stable equilibrium.
OK, but that can be just lucky - how lucky depends on your preparation
protocol, which you haven't told us about. You are not actually doing
the same calculation on both machines - the processes are chaotic even
if everything seems equivalent.
On the cluster, it appears stable until step 14555 where I get LINCS
warnings such as
Those warnings look pretty localized to a region of your structure.
Firstly, some kind of linking or GROMACS failure would be likely to be
manifest all over the place - and cause problems even if you did a run
with different velocity generation. Secondly, have you looked at the
resulting PDB files? You may wish to run the simulation to step 14500,
and then restart with nstxout=1 so you can watch it explode. That may
highlight a bad contact suddenly being able to relax.
Mark
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
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