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On 13/07/2011 7:01 PM, Luke Goodsell wrote:
<blockquote
cite="mid:CAF=S613rrGi9oZjcxkaVHy4tu26aiOoSsM4M_pX5iip=NVEFaA@mail.gmail.com"
type="cite">Hi Mark,
<div><br>
</div>
<div>
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Perhaps your simulation is intrinsically unstable, and you
haven't gotten unlucky enough yet on the iMac. Check out <a
moz-do-not-send="true"
href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up"
target="_blank">http://www.gromacs.org/Documentation/Terminology/Blowing_Up</a><br>
</blockquote>
<div> </div>
<div>The simulation on the iMac reaches a stable equilibrium.
</div>
</div>
</div>
</blockquote>
<br>
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.<br>
<br>
<blockquote
cite="mid:CAF=S613rrGi9oZjcxkaVHy4tu26aiOoSsM4M_pX5iip=NVEFaA@mail.gmail.com"
type="cite">
<div>
<div class="gmail_quote">
<div>On the cluster, it appears stable until step 14555 where
I get LINCS warnings such as</div>
</div>
</div>
</blockquote>
<br>
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.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAF=S613rrGi9oZjcxkaVHy4tu26aiOoSsM4M_pX5iip=NVEFaA@mail.gmail.com"
type="cite">
<div>
<div class="gmail_quote">
<div><br>
</div>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Step 14555, time 29.11 (ps) LINCS WARNING</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
relative constraint deviation after LINCS:</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
rms 0.078151, max 2.416183 (between atoms 1720 and 1721)</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
bonds that rotated more than 30 degrees:</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
atom 1 atom 2 angle previous, current, constraint
length</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1720 1721 151.3 0.1080 0.3689 0.1080</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1707 1708 152.8 0.1090 0.3674 0.1090</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Wrote pdb files with previous and current coordinates</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<br>
</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Step 14555, time 29.11 (ps) LINCS WARNING</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
relative constraint deviation after LINCS:</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
rms 0.078245, max 2.420384 (between atoms 1720 and 1721)</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
bonds that rotated more than 30 degrees:</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
atom 1 atom 2 angle previous, current, constraint
length</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1720 1721 151.3 0.1080 0.3694 0.1080</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1707 1708 152.8 0.1090 0.3676 0.1090</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<br>
</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Back Off! I just backed up step14555b.pdb to
./#step14555b.pdb.1#</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<br>
</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Back Off! I just backed up step14555c.pdb to
./#step14555c.pdb.1#</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Wrote pdb files with previous and current coordinates</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<br>
</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Step 14556, time 29.112 (ps) LINCS WARNING</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
relative constraint deviation after LINCS:</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
rms 133.212808, max 5757.494141 (between atoms 1720 and
1721)</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
bonds that rotated more than 30 degrees:</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
atom 1 atom 2 angle previous, current, constraint
length</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1722 1724 36.7 0.1336 0.1716 0.1335</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1722 1723 35.5 0.1230 0.1553 0.1229</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1720 1721 90.0 0.3694 621.9174 0.1080</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1718 1720 144.9 0.1407 0.5335 0.1400</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1718 1719 105.6 0.1085 1.0804 0.1080</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1716 1717 90.6 0.0960 24.8478 0.0960</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1715 1718 136.5 0.1414 0.4281 0.1409</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1715 1716 90.6 0.1366 37.5311 0.1364</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1713 1715 111.6 0.1412 1.0479 0.1409</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1713 1714 120.7 0.1082 0.3603 0.1080</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1711 1713 118.7 0.1402 0.3129 0.1400</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1711 1712 53.9 0.1082 0.1451 0.1080</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1710 1720 101.0 0.1407 1.7692 0.1400</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1710 1711 57.8 0.1404 0.2418 0.1400</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1707 1710 112.0 0.1520 0.5543 0.1510</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1707 1709 107.4 0.1098 0.5075 0.1090</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1707 1708 102.7 0.3676 1.4700 0.1090</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1705 1722 75.1 0.1525 0.2535 0.1522</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1705 1707 106.7 0.1533 0.6142 0.1526</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1705 1706 56.4 0.1093 0.1136 0.1090</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1703 1705 89.0 0.1452 0.2683 0.1449</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1703 1704 42.3 0.1010 0.1384 0.1010</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1701 1703 38.9 0.1336 0.1768 0.1335</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1673 1674 35.7 0.1229 0.1230 0.1229</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1670 1673 31.2 0.1522 0.1523 0.1522</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Wrote pdb files with previous and current coordinates</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<br>
</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Step 14556, time 29.112 (ps) LINCS WARNING</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
relative constraint deviation after LINCS:</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
rms 133.228686, max 5758.184082 (between atoms 1720 and
1721)</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
bonds that rotated more than 30 degrees:</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
atom 1 atom 2 angle previous, current, constraint
length</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1722 1724 47.6 0.1336 0.1995 0.1335</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1722 1723 45.8 0.1230 0.1781 0.1229</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1720 1721 90.0 0.3694 621.9919 0.1080</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1718 1720 141.7 0.1407 0.5243 0.1400</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1718 1719 106.2 0.1085 1.1444 0.1080</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1716 1717 90.7 0.0960 24.8269 0.0960</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1715 1718 144.6 0.1414 0.5103 0.1409</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1715 1716 90.6 0.1366 37.5424 0.1364</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1713 1715 112.9 0.1412 1.0642 0.1409</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1713 1714 120.9 0.1082 0.3765 0.1080</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1711 1713 124.0 0.1402 0.2954 0.1400</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1711 1712 52.5 0.1082 0.1399 0.1080</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1710 1720 103.1 0.1407 1.8233 0.1400</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1710 1711 75.5 0.1404 0.2584 0.1400</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1707 1710 117.5 0.1520 0.6407 0.1510</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1707 1709 109.9 0.1098 0.6153 0.1090</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1707 1708 102.2 0.3676 1.5528 0.1090</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1705 1722 92.4 0.1525 0.2917 0.1522</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1705 1707 107.2 0.1533 0.7484 0.1526</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1705 1706 57.0 0.1093 0.0958 0.1090</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1703 1705 94.4 0.1452 0.3185 0.1449</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1703 1704 49.7 0.1010 0.1528 0.1010</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1701 1703 46.6 0.1336 0.1937 0.1335</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1673 1674 35.7 0.1229 0.1230 0.1229</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
1670 1673 31.2 0.1522 0.1523 0.1522</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<br>
</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Back Off! I just backed up step14556b.pdb to
./#step14556b.pdb.1#</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<br>
</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Back Off! I just backed up step14556c.pdb to
./#step14556c.pdb.1#</blockquote>
<blockquote class="gmail_quote" style="margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
Wrote pdb files with previous and current coordinates</blockquote>
</blockquote>
<div><br>
</div>
<div>The system is 'blowing up', no (rms ~575.8nm between 1720
and 1721)?</div>
<meta charset="utf-8">
<div><br>
</div>
<div>
It appears to me that there is some significant difference
in the operation of gromacs in the two environments.</div>
<div><br>
</div>
<div>Thanks,</div>
<div>Luke</div>
</div>
</div>
</blockquote>
<br>
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