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Hi,<br>
<br>
Please keep such discussions on the mailing list so that others can
learn and contribute from the discussion and its archive.<br>
<br>
On point, this .mdp file has a feature about which I have already
indicated a link that highlights its undesirability. Moreover, this
.mdp file did not produce the simulation that crashed, because
you've previously reported the same output from a different .mdp
file. That kind of mismatch makes it hard for people to want to
help...<br>
<br>
The link Justin provided originally has tips on how to diagnose what
is going wrong on systems that are blowing up. You should read that
link and follow links from it. In the absence of new information
from you, there's really nothing else that we can help with.<br>
<br>
Mark<br>
<br>
-------- Original Message --------
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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">Subject: </th>
<td>Check for bad contacts and/or reduce the timestep</td>
</tr>
<tr>
<th align="RIGHT" nowrap="nowrap" valign="BASELINE">Date: </th>
<td>Fri, 09 Dec 2011 13:28:41 +0530</td>
</tr>
<tr>
<th align="RIGHT" nowrap="nowrap" valign="BASELINE">From: </th>
<td>pragna lakshmi <a class="moz-txt-link-rfc2396E" href="mailto:pragnapcu@gmail.com"><pragnapcu@gmail.com></a></td>
</tr>
<tr>
<th align="RIGHT" nowrap="nowrap" valign="BASELINE">To: </th>
<td><a class="moz-txt-link-abbreviated" href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a></td>
</tr>
</tbody>
</table>
<br>
<br>
Dear Mark,
<div> i am trying to do protein-ligand simulation.
while running energy minimization step maximum force is on atom
2099. And it was completed in 696 steps. I used pr.mdp file for
equilibration which is given below.</div>
<div><span
style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse;color:rgb(34,34,34)">
<div>
<div><br>
</div>
<div>title = protein</div>
<div>cpp = /lib/cpp ; location of cpp on SGI</div>
<div>define = -DPOSRES</div>
<div>constraints = all-bonds</div>
<div>integrator = md</div>
<div>dt = 0.002 ; ps !</div>
<div>nsteps = 50000 ; total 20.0 ps.</div>
<div>nstcomm = 1</div>
<div>nstxout = 250 ; output coordinates every 0.5 ps</div>
<div>nstvout = 1000 ; output velocities every 2.0 ps</div>
<div>nstfout = 0</div>
<div>nstlog = 10</div>
<div>nstenergy = 10</div>
<div>nstlist = 10</div>
<div>ns_type = grid</div>
<div>rlist = 0.9</div>
<div>coulombtype = PME</div>
<div>rcoulomb = 0.9</div>
<div>rvdw = 1.0</div>
<div>fourierspacing = 0.12</div>
<div>fourier_nx = 0</div>
<div>fourier_ny = 0</div>
<div>fourier_nz = 0</div>
<div>pme_order = 6</div>
<div>ewald_rtol = 1e-5</div>
<div>optimize_fft = yes</div>
<div>; Berendsen temperature coupling is on in four groups</div>
<div>Tcoupl = V-rescale</div>
<div>tau_t = 0.1 0.1 0.1 0.1 0.1</div>
<div>tc_grps = protein ZN sol IMP NA+</div>
<div>ref_t = 300 300 300 300 300</div>
<div>; Pressure coupling is on</div>
<div>Pcoupl = no</div>
<div>pcoupltype = isotropic</div>
<div>tau_p = 0.5</div>
<div>compressibility = 4.5e-5</div>
<div>ref_p = 1.0</div>
<div>; Generate velocites is on at 300 K.</div>
<div>gen_vel = yes</div>
<div>gen_temp = 300.0</div>
<div>gen_seed = 173529</div>
</div>
<div><br>
</div>
<div> pr.mdp step run
well. But at final md step it is showing the following error. </div>
<div><br>
</div>
<div>
<div>Step 105692, time 211.384 (ps) LINCS WARNING</div>
<div>relative constraint deviation after LINCS:</div>
<div>rms 0.002880, max 0.071917 (between atoms 2097 and 2095)</div>
<div>bonds that rotated more than 30 degrees:</div>
<div> atom 1 atom 2 angle previous, current, constraint
length</div>
<div> 2098 2099 38.6 0.1330 0.1371 0.1330</div>
<div> 2097 2098 45.2 0.1330 0.1370 0.1330</div>
<div>.</div>
<div>.</div>
<div>.</div>
<div>.</div>
<div>
<div>Step 226039, time 452.078 (ps) LINCS WARNING</div>
<div>relative constraint deviation after LINCS:</div>
<div>rms 42.444550, max 1059.016235 (between atoms 2098 and
2099)</div>
<div>bonds that rotated more than 30 degrees:</div>
<div> atom 1 atom 2 angle previous, current, constraint
length</div>
<div> 2095 2094 31.6 0.1441 10.5310 0.1250</div>
<div> 2113 2114 40.8 0.1471 0.1950 0.1470</div>
<div> 2117 2112 36.4 0.1521 0.1902 0.1520</div>
<div> 2111 2113 81.7 0.1535 0.2949 0.1520</div>
<div> 2111 2112 83.9 0.1534 0.2900 0.1520</div>
<div> 2111 2110 113.2 0.1833 0.8261 0.1780</div>
<div> 2109 2110 43.8 0.2063 11.5418 0.1750</div>
<div> 2107 2109 38.3 0.1516 11.2487 0.1390</div>
<div> 2107 2108 103.0 0.1581 11.5450 0.1530</div>
<div> 2106 2107 77.4 0.1333 30.0780 0.1530</div>
<div> 2104 2105 140.0 0.1080 2.2354 0.1000</div>
<div> 2102 2104 34.2 0.1426 16.8737 0.1430</div>
<div> 2102 2103 89.9 0.1637 15.4076 0.1530</div>
<div> 2101 2106 142.0 0.2077 63.6808 0.1530</div>
<div> 2101 2102 132.5 0.1659 62.8960 0.1530</div>
<div> 2101 2099 174.7 0.5646 127.3807 0.1390</div>
<div> 2099 2100 160.1 0.5219 101.4140 0.1230</div>
<div> 2106 2098 166.3 0.2022 76.2729 0.1480</div>
<div> 2098 2099 174.8 0.6156 140.9822 0.1330</div>
<div> 2097 2109 149.5 0.1057 36.9859 0.1330</div>
<div> 2097 2098 159.4 0.2818 84.7773 0.1330</div>
<div> 2097 2095 164.8 0.1042 37.0501 0.1330</div>
<div> 2095 2096 70.7 0.1482 9.8470 0.1250</div>
<div>Wrote pdb files with previous and current coordinates</div>
<div>There were 4 inconsistent shifts. Check your topology</div>
<div>Warning: 1-4 interaction between 2094 and 2098 at
distance 44.117 which is larger than the 1-4 table size
2.000 nm</div>
<div>These are ignored for the rest of the simulation</div>
<div>This usually means your system is exploding,</div>
<div>if not, you should increase table-extension in your mdp
file</div>
<div>or with user tables increase the table size</div>
</div>
<div>.</div>
<div>.</div>
<div>.</div>
<div>.</div>
<div>
<div> 1416 1417 89.7 0.1530 705915256832.0000
0.1530</div>
<div> 1414 1416 90.4 0.1470 419510747136.0000
0.1470</div>
<div> 1414 1415 92.3 0.1000 45284384768.0000
0.1000</div>
<div> 1412 1414 89.5 0.1330 55051784192.0000
0.1330</div>
<div> 1412 1413 106.4 0.1230 13457604608.0000
0.1230</div>
<div> 1409 1411 119.2 0.1530 519590400.0000
0.1530</div>
<div> 1409 1410 107.4 0.1530 519590400.0000
0.1530</div>
<div> 1408 1412 99.1 0.1530 14933683200.0000
0.1530</div>
<div> 1408 1409 98.3 0.1530 4102264576.0000
0.1530</div>
<div> 1406 1408 98.5 0.1470 4076032256.0000
0.1470</div>
<div> 1406 1407 107.8 0.1000 606216384.0000
0.1000</div>
<div> 1404 1406 122.9 0.1330 606216384.0000
0.1330</div>
<div> 1404 1405 31.5 0.1230 0.1567 0.1230</div>
<div> 2120 2122 105.2 0.1473 84501076367114240.0000
0.1470</div>
<div> 2120 2121 105.8 0.1473 83934295302864896.0000
0.1470</div>
<div> 2118 2120 95.0 0.1349 219396825084329984.0000
0.1340</div>
<div> 2118 2119 96.0 0.1236 223179042004664320.0000
0.1230</div>
<div><br>
</div>
<div>t = 452.080 ps: Water molecule starting at atom 36608
can not be settled.</div>
<div>Check for bad contacts and/or reduce the timestep.</div>
<div>Wrote pdb files with previous and current coordinates</div>
<div>Segmentation fault (core dumped)</div>
</div>
</div>
<div><br>
</div>
</span>
<div><span class="Apple-style-span" style="font-family: arial,
sans-serif; font-size: 13px; border-collapse: collapse; color:
rgb(34, 34, 34); ">I understood that the force is maximum on
atom 2099 and it might be the reason for this problem. i have
gone through this link. But i am really fail to trouble shoot
this error. Could you please help me out in getting solution
for this problem. I have been trying different ways to solve
it out. But nothing went well. I am Sorry for mailing you
personally.</span></div>
<div><span class="Apple-style-span" style="font-family: arial,
sans-serif; font-size: 13px; border-collapse: collapse; color:
rgb(34, 34, 34); "><br>
</span></div>
-- <br>
<div style="line-height:normal"><span
style="font-family:"Times New
Roman","serif";font-size:12pt">T.Pragna
Lakshmi,</span></div>
<div style="line-height:normal"><span
style="font-family:"Times New
Roman","serif";font-size:12pt">Junior
Scientist,</span></div>
<div style="line-height:normal"><span
style="font-family:"Times New
Roman","serif";font-size:12pt"><span
style="font-family:"Times New
Roman","serif";font-size:12pt">Vision
Research Center,</span></span></div>
<div style="line-height:normal"><span
style="font-family:"Times New
Roman","serif";font-size:12pt">Sankara
Netralaya,</span></div>
<div style="line-height:normal"><span
style="font-family:"Times New
Roman","serif";font-size:12pt">Chennai,</span></div>
<div style="line-height:normal"><span
style="font-family:"Times New
Roman","serif";font-size:12pt">India.</span></div>
<div style="line-height:normal"><span
style="font-family:"Times New
Roman","serif";font-size:12pt">Pin: 600006.</span></div>
<br>
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