On 23/03/2011 9:45 PM, Anna Marabotti wrote:
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?
Usually the problem has nothing to do with LINCS or -rdd or -con -
they're just symptoms of machinery that breaks first.
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.
Mark
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