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<DIV><FONT size=2 face=Arial><SPAN class=437311710-23032011>Dear
gmx-users,</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN class=437311710-23032011>I'm experimenting a
LINCS warning on my system, an enzyme with ATP, galactose and Mg. We started
from the crystallographic structure, made some accommodation on the topology of
the sugar in order to check for partial charges (according to Justin Lemkul's
suggestions on PRODRG server), then performed a minimization, NVT and NPT PR-MD
and the production MD. After about 5 ns of simulation the MD stopped with the
LINCS error:</SPAN></FONT></DIV>
<DIV><FONT size=2 face=Arial><SPAN
class=437311710-23032011></SPAN></FONT> </DIV>
<DIV><SPAN class=437311710-23032011><SPAN lang=IT>
<P><FONT size=2 face=Arial>Step 2562553, time 5125.11 (ps) LINCS
WARNING</FONT></P>
<P><FONT size=2 face=Arial>relative constraint deviation after LINCS:</FONT></P>
<P><FONT size=2 face=Arial>rms 0.000102, max 0.001903 (between atoms 7643 and
7642)</FONT></P>
<P><FONT size=2 face=Arial>bonds that rotated more than 30 degrees:</FONT></P>
<P><FONT size=2 face=Arial>atom 1 atom 2 angle previous, current, constraint
length</FONT></P>
<P><FONT size=2 face=Arial>7641 7640 45.3 0.1000 0.1000 0.1000</FONT></P>
<P><FONT size=2 face=Arial>Step 2562554, time 5125.11 (ps) LINCS
WARNING</FONT></P>
<P><FONT size=2 face=Arial>relative constraint deviation after LINCS:</FONT></P>
<P><FONT size=2 face=Arial>rms 0.000104, max 0.001558 (between atoms 7643 and
7642)</FONT></P>
<P><FONT size=2 face=Arial>bonds that rotated more than 30 degrees:</FONT></P>
<P><FONT size=2 face=Arial>atom 1 atom 2 angle previous, current, constraint
length</FONT></P>
<P><FONT size=2 face=Arial>7641 7640 36.5 0.1000 0.1000 0.1000</FONT></P>
<P><FONT size=2 face=Arial>Step 2562565, time 5125.13 (ps) LINCS
WARNING</FONT></P>
<P><FONT size=2 face=Arial>relative constraint deviation after LINCS:</FONT></P>
<P><FONT size=2 face=Arial>rms 0.000318, max 0.007712 (between atoms 7641 and
7640)</FONT></P>
<P><FONT size=2 face=Arial>bonds that rotated more than 30 degrees:</FONT></P>
<P><FONT size=2 face=Arial>atom 1 atom 2 angle previous, current, constraint
length</FONT></P>
<P><FONT size=2 face=Arial>7641 7640 31.5 0.1005 0.1008 0.1000</FONT></P>
<P><FONT size=2 face=Arial>Step 2562566, time 5125.13 (ps) LINCS
WARNING</FONT></P>
<P><FONT size=2 face=Arial>relative constraint deviation after LINCS:</FONT></P>
<P><FONT size=2 face=Arial>rms 0.000374, max 0.009231 (between atoms 7641 and
7640)</FONT></P>
<P><FONT size=2 face=Arial>bonds that rotated more than 30 degrees:</FONT></P>
<P><FONT size=2 face=Arial>atom 1 atom 2 angle previous, current, constraint
length</FONT></P>
<P><FONT size=2 face=Arial>7641 7640 38.2 0.1008 0.1009 0.1000</FONT></P>
<P><FONT size=2 face=Arial>Step 2562567, time 5125.13 (ps) LINCS
WARNING</FONT></P>
<P><FONT size=2 face=Arial>relative constraint deviation after LINCS:</FONT></P>
<P><FONT size=2 face=Arial>rms 0.000310, max 0.007658 (between atoms 7641 and
7640)</FONT></P>
<P><FONT size=2 face=Arial>bonds that rotated more than 30 degrees:</FONT></P>
<P><FONT size=2 face=Arial>atom 1 atom 2 angle previous, current, constraint
length</FONT></P>
<P><FONT size=2 face=Arial>7641 7640 38.6 0.1009 0.1008 0.1000</FONT></P>
<P><SPAN class=437311710-23032011><FONT size=2
face=Arial>............................................................</FONT></SPAN></P><SPAN
class=437311710-23032011><SPAN lang=IT>
<P>Step 2563563, time 5127.13 (ps) LINCS WARNING</P>
<P>relative constraint deviation after LINCS:</P>
<P>rms 0.000070, max 0.001640 (between atoms 7641 and 7640)</P>
<P>bonds that rotated more than 30 degrees:</P>
<P>atom 1 atom 2 angle previous, current, constraint length</P>
<P>7641 7640 57.0 0.0998 0.1002 0.1000</P>
<P>-------------------------------------------------------</P>
<P>Program mdrun, VERSION 4.0.3</P>
<P>Source code file: constr.c, line: 136</P>
<P>Fatal error:</P>
<P>Too many LINCS warnings (1000)</P>
<P>If you know what you are doing you can adjust the lincs warning threshold in
your mdp file</P>
<P>or set the environment variable GMX_MAXCONSTRWARN to -1,</P>
<P>but normally it is better to fix the problem</P>
<P>-------------------------------------------------------</P></SPAN></SPAN></SPAN></SPAN></DIV>
<DIV><SPAN class=437311710-23032011><FONT size=2 face=Arial>We checked the
system to find the problem. The atoms 7641 and 7640 correspond to atom O1 and
H12 of the galactose. With VMD we visualized the trajectory, but we did not see
anything anomalous on this bond. Length and angles are quite normal. This OH
group is near the phosphate of ATP but the distances seem to be compatible with
an (expected) H-bond. I don't think the problem could be an incorrect
stabilization because it seems to me that in that case the problem would have
appear during the first step of MD, not after 5 ns. In any case, stabilization
went correctly, with no errors or warnings. I checked on the gmx-users list and
found some messages of Xavier Periole experimenting some LINCS problems with gmx
4.0.4, that seems to resemble my situation. I followed the thread, but I
did not see anything that could be of help for me. Some hypotheses were about
the gmx version (mine is 4.0.3), communications between CPUs, virtual sites.
Looking at the trajectory, I don't think it's a problem of periodic images
too close. The thread stops with Xavier saying he would like to test the
effects of using -rdd and -rcon on LINCS warning, but I did not find the rest of
the history. </FONT></SPAN></DIV>
<DIV><SPAN class=437311710-23032011><FONT size=2
face=Arial></FONT></SPAN> </DIV>
<DIV><SPAN class=437311710-23032011><FONT size=2 face=Arial>Does anybody (and
especially Xavier, if possible!) have some hints about my problem? Or could it
be a problem of galactose topology?</FONT></SPAN></DIV>
<DIV><SPAN class=437311710-23032011></SPAN> </DIV>
<DIV><SPAN class=437311710-23032011><FONT size=2 face=Arial>Thank you very much
and best regards</FONT></SPAN></DIV>
<DIV><SPAN class=437311710-23032011><FONT size=2
face=Arial>Anna</FONT> </SPAN></DIV>
<DIV align=left>
<DIV dir=ltr align=left><FONT size=2
face=Arial>__________________________________________________________________</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Anna Marabotti, Ph.D.</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Laboratory of Bioinformatics and
Computational Biology</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Institute of Food Science -
CNR</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Via Roma, 64</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>83100 Avellino</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Phone: +39 0825 299651</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Fax: +39 0825 781585</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>E-mail: <A
title=mailto:amarabotti@isa.cnr.it
href="mailto:amarabotti@isa.cnr.it">amarabotti@isa.cnr.it</A></FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Skype account: annam1972</FONT></DIV>
<DIV align=left><FONT size=2 face=Arial>Web site: <A
title=http://bioinformatica.isa.cnr.it/anna/anna.htm
href="http://bioinformatica.isa.cnr.it/anna/anna.htm">http://bioinformatica.isa.cnr.it/anna/anna.htm</A></FONT></DIV>
<DIV align=left><FONT size=2 face=Arial></FONT> </DIV>
<DIV align=left><FONT size=2 face=Arial>"When a man with a gun meets a man with
a pen, the man with the gun is a dead man"</FONT></DIV></DIV>
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