[gmx-users] Essential Dynamics lincs warning

Sai Pooja saipooja at gmail.com
Tue Apr 12 21:17:00 CEST 2011


I am running essential dynamics for a protein in water system (charmm-nocmap
and tip3p). I use the first 25 eigenvectors and targeted ED. It stops after
630ps when settle and lincs start giving warnings.

Step 315573, time 631.146 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000121, max 0.003164 (between atoms 144 and 145)
bonds that rotated more than 30 degrees:
 atom 1 atom 2  angle  previous, current, constraint length
   148    151   36.2    0.1112   0.1111      0.1111
   144    145   45.7    0.1109   0.1107      0.1111

I am also running the same simulation with the first 12 eigenvectors and
face no such problems.

I understand that targeted ED may lead to some unphysical trajectory which
may be the cause of this error. However, is there a way to override this and
in that case an alternative check which may be used instead of lincs
rotation constraint to make sure that the contacts arent unphysical?


Quaerendo Invenietis-Seek and you shall discover.
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