[gmx-users] LINCS warning on galactose molecule

[Anna Marabotti]

Dear gmx-users,
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:
 
Step 2562553, time 5125.11 (ps) LINCS WARNING

relative constraint deviation after LINCS:

rms 0.000102, max 0.001903 (between atoms 7643 and 7642)

bonds that rotated more than 30 degrees:

atom 1 atom 2 angle previous, current, constraint length

7641 7640 45.3 0.1000 0.1000 0.1000

Step 2562554, time 5125.11 (ps) LINCS WARNING

relative constraint deviation after LINCS:

rms 0.000104, max 0.001558 (between atoms 7643 and 7642)

bonds that rotated more than 30 degrees:

atom 1 atom 2 angle previous, current, constraint length

7641 7640 36.5 0.1000 0.1000 0.1000

Step 2562565, time 5125.13 (ps) LINCS WARNING

relative constraint deviation after LINCS:

rms 0.000318, max 0.007712 (between atoms 7641 and 7640)

bonds that rotated more than 30 degrees:

atom 1 atom 2 angle previous, current, constraint length

7641 7640 31.5 0.1005 0.1008 0.1000

Step 2562566, time 5125.13 (ps) LINCS WARNING

relative constraint deviation after LINCS:

rms 0.000374, max 0.009231 (between atoms 7641 and 7640)

bonds that rotated more than 30 degrees:

atom 1 atom 2 angle previous, current, constraint length

7641 7640 38.2 0.1008 0.1009 0.1000

Step 2562567, time 5125.13 (ps) LINCS WARNING

relative constraint deviation after LINCS:

rms 0.000310, max 0.007658 (between atoms 7641 and 7640)

bonds that rotated more than 30 degrees:

atom 1 atom 2 angle previous, current, constraint length

7641 7640 38.6 0.1009 0.1008 0.1000

............................................................

Step 2563563, time 5127.13 (ps) LINCS WARNING

relative constraint deviation after LINCS:

rms 0.000070, max 0.001640 (between atoms 7641 and 7640)

bonds that rotated more than 30 degrees:

atom 1 atom 2 angle previous, current, constraint length

7641 7640 57.0 0.0998 0.1002 0.1000

-------------------------------------------------------

Program mdrun, VERSION 4.0.3

Source code file: constr.c, line: 136

Fatal error:

Too many LINCS warnings (1000)

If you know what you are doing you can adjust the lincs warning threshold in
your mdp file

or set the environment variable GMX_MAXCONSTRWARN to -1,

but normally it is better to fix the problem

-------------------------------------------------------

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.

 
Does anybody (and especially Xavier, if possible!) have some hints about my
problem? Or could it be a problem of galactose topology?
 
Thank you very much and best regards
Anna 
__________________________________________________________________
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science - CNR
Via Roma, 64
83100 Avellino
Phone: +39 0825 299651
Fax: +39 0825 781585
E-mail: amarabotti at isa.cnr.it
Skype account: annam1972
Web site: http://bioinformatica.isa.cnr.it/anna/anna.htm
 
"When a man with a gun meets a man with a pen, the man with the gun is a
dead man"
 
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