[gmx-users] Structural features for LINCS application

Francesco Oteri francesco.oteri at gmail.com
Thu Mar 15 20:02:43 CET 2012

Dear gromacs users,
I am trying to simulate a protein (containing FeS cluster and a complex 
metal active site) using virtual site.
I've to face a problem with LINCS. In particular, if I constrain only 
h-bonds without using virtual site,
simulation runs fine but constraining "all-bonds", simulation crashes 
after a lot of LINCS warning like:

Step 356, time 0.712 (ps)  LINCS WARNING
relative constraint deviation after LINCS:
rms 0.408533, max 8.159325 (between atoms 2750 and 2754)
bonds that rotated more than 30 degrees:
  atom 1 atom 2  angle  previous, current, constraint length
    2750   2754   90.0    0.1365   1.2502      0.1365

In both cases simulation conditions are the same. The bonds causing 
problem belongs to the active site.
I am wondering if there are structural features imparing the use of 
all-bonds constraints in LINCS.
A second question is, how can I run MD with virtual site without 
all-bonds options.

Thank you,

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