My simulation aborts rather quickly because it accumulates too many
LINCS warning. I checked the various plots and everything seems to be
stable (temperature, pressure, total energy, etc.). The stderr gives
me warnings looking like this:
Step 2304252, time 4608.5 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.043352, max 0.606635 (between atoms 150 and 151)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
150 152 90.0 0.0985 0.1490 0.1000
150 151 90.0 0.1314 0.1607 0.1000
The problem I see is that atom 150 and 151 do not even have a bond
between them (they are the two hydrogens of one water molecule). I
also get similar warning between 150 and 152, which are not even on
the same water molecule. I have extensively equilibrated the system as
I thought that it was the problem originally.
Anyone here has an intuition as to why this may happen?
Thanks,
Christian
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
