Justin,<br><br>I've minimised my system to emtool=1.0<br>but the error still occurs<br><br><br><div class="gmail_quote">31 อมาิม 2012ว. 16:27 ะฯฬฺุฯืมิลฬุ Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> ฮมะษำมฬ:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class="im"><br></div>
Separate COM motion removal groups are tricky. I'm still not completely clear on what your system looks like, but if you've got two proteins in two layers of solvent and you expect one or both of them to move in such a way that they begin to interact, it may not be appropriate to be using the groups you've shown below.</blockquote>
<div><br>My system consist of membrane receptor in membrane-like bilayer surrounded by water. Also part of the receptor is in the water layer. To this part wich are in the water another water-soluble protein ( part of the G-protein) has been attached.<br>
</div><div><br></div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="im"></div>
And what was the exact outcome?</blockquote><div><br>This is the error log<br><br>Getting Loaded...<br>Reading file nvt.tpr, VERSION 4.5.4 (single precision)<br>Loaded with Money<br><br><br>Step 0, time 0 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>rms 0.002373, max 0.102422 (between atoms 1387 and 1388)<br>bonds that rotated more than 30 degrees:<br>atom 1 atom 2 angle previous, current, constraint length<br>starting mdrun 'B2ar_in_Ccl4 in water'<br>
500000 steps, 1000.0 ps.<br><br>Step 0, time 0 (ps) LINCS WARNING<br>relative constraint deviation after LINCS:<br>rms 73.552702, max 3051.386475 (between atoms 8551 and 8552)<br>bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br> 1407 1412 34.8 0.1530 0.1955 0.1530<br> 1407 1408 35.2 0.1530 0.1943 0.1530<br> 1405 1407 152.5 0.1471 0.1638 0.1470<br>
1405 1406 123.6 0.1001 0.2394 0.1000<br>etc - the above- part of atoms of the first protein<br><br><br> 8519 8520 44.3 0.1001 0.1498 0.1000<br> 8517 8519 41.6 0.1331 0.1901 0.1330<br>
8478 8480 54.9 0.1330 0.1555 0.1330<br> 8478 8479 44.8 0.1230 0.1262 0.1230<br> 8465 8478 52.7 0.1530 0.1491 0.1530<br>this is part of atoms of the second protein<br><br><br>
Also I've attached my nvt.mdp file<br><br>in this file<br>a_1-4232 is the first protein<br>a_8365-8643 is the second protein.<br><br><br>What's wrong with this system?<br><br>James<br><br><br><br></div></div>