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<DIV><FONT face=Arial size=2>Hi,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>I am simulating a system of infinite polymer chains
using pbc=full and LINCS bond constraints. </FONT></DIV>
<DIV><FONT face=Arial size=2>My system is unreliable and sometimes the
simulations crash due to LINCS complaining about too large
bond rotations. </FONT></DIV>
<DIV><FONT face=Arial size=2>I have now noted that it seems like LINCS gives
warnings of the kind:</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Step 22525, time 67.575 (ps) LINCS
WARNING<BR>relative constraint deviation after LINCS:<BR>max 0.000029 (between
atoms 22 and 23) rms 0.000004<BR>bonds that rotated more than 30
degrees:<BR> atom 1 atom 2 angle previous, current, constraint
length<BR> 347 348
30.6 0.1000 0.1000
0.1000</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>and the atoms are always situated on different
sides of a periodic bound. A question that now arises is whether this could
be a bug with pbc=full or whether there is a problem with my system. I am
using Gromacs 3.3.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Any suggestions about how I could check this or
whatever about whatever the problem could be I would be grateful.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Best regards,</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Malin</DIV>
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