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On 23/03/2011 9:45 PM, Anna Marabotti wrote:
<blockquote cite="mid:8AE8EEFCC279432A9C1675D2BB787B62@AnnaNetbook"
type="cite">
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<div><font face="Arial" size="2"><span class="437311710-23032011">Dear
gmx-users,</span></font></div>
<div><font face="Arial" size="2"><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 face="Arial" size="2"><span class="437311710-23032011"></span></font> </div>
<div><span class="437311710-23032011"><span lang="IT">
<p><font face="Arial" size="2">Step 2562553, time 5125.11
(ps) LINCS WARNING</font></p>
<p><font face="Arial" size="2">relative constraint deviation
after LINCS:</font></p>
<p><font face="Arial" size="2">rms 0.000102, max 0.001903
(between atoms 7643 and 7642)</font></p>
<p><font face="Arial" size="2">bonds that rotated more than
30 degrees:</font></p>
<p><font face="Arial" size="2">atom 1 atom 2 angle previous,
current, constraint length</font></p>
<p><font face="Arial" size="2">7641 7640 45.3 0.1000 0.1000
0.1000</font></p>
<p><font face="Arial" size="2">Step 2562554, time 5125.11
(ps) LINCS WARNING</font></p>
<p><font face="Arial" size="2">relative constraint deviation
after LINCS:</font></p>
<p><font face="Arial" size="2">rms 0.000104, max 0.001558
(between atoms 7643 and 7642)</font></p>
<p><font face="Arial" size="2">bonds that rotated more than
30 degrees:</font></p>
<p><font face="Arial" size="2">atom 1 atom 2 angle previous,
current, constraint length</font></p>
<p><font face="Arial" size="2">7641 7640 36.5 0.1000 0.1000
0.1000</font></p>
<p><font face="Arial" size="2">Step 2562565, time 5125.13
(ps) LINCS WARNING</font></p>
<p><font face="Arial" size="2">relative constraint deviation
after LINCS:</font></p>
<p><font face="Arial" size="2">rms 0.000318, max 0.007712
(between atoms 7641 and 7640)</font></p>
<p><font face="Arial" size="2">bonds that rotated more than
30 degrees:</font></p>
<p><font face="Arial" size="2">atom 1 atom 2 angle previous,
current, constraint length</font></p>
<p><font face="Arial" size="2">7641 7640 31.5 0.1005 0.1008
0.1000</font></p>
<p><font face="Arial" size="2">Step 2562566, time 5125.13
(ps) LINCS WARNING</font></p>
<p><font face="Arial" size="2">relative constraint deviation
after LINCS:</font></p>
<p><font face="Arial" size="2">rms 0.000374, max 0.009231
(between atoms 7641 and 7640)</font></p>
<p><font face="Arial" size="2">bonds that rotated more than
30 degrees:</font></p>
<p><font face="Arial" size="2">atom 1 atom 2 angle previous,
current, constraint length</font></p>
<p><font face="Arial" size="2">7641 7640 38.2 0.1008 0.1009
0.1000</font></p>
<p><font face="Arial" size="2">Step 2562567, time 5125.13
(ps) LINCS WARNING</font></p>
<p><font face="Arial" size="2">relative constraint deviation
after LINCS:</font></p>
<p><font face="Arial" size="2">rms 0.000310, max 0.007658
(between atoms 7641 and 7640)</font></p>
<p><font face="Arial" size="2">bonds that rotated more than
30 degrees:</font></p>
<p><font face="Arial" size="2">atom 1 atom 2 angle previous,
current, constraint length</font></p>
<p><font face="Arial" size="2">7641 7640 38.6 0.1009 0.1008
0.1000</font></p>
<p><span class="437311710-23032011"><font face="Arial"
size="2">............................................................</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 face="Arial" size="2">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"></span> </div>
<div><span class="437311710-23032011"><font face="Arial" size="2">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>
</blockquote>
<br>
Usually the problem has nothing to do with LINCS or -rdd or -con -
they're just symptoms of machinery that breaks first.<br>
<br>
I'd start by assuming my topologies were not well-formed somehow,
and divide and conquer to locate the problem. Can you simulate
galactose in vacuo? In a small water box? Same for ATP. Same for
enzyme.<br>
<br>
Mark<br>
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