[gmx-users] LINCS warning

neda mirsamadi nedamirsamadi at yahoo.com
Mon Sep 6 08:24:20 CEST 2004

Dear GMX users
I am trying to simulate a protein which has four
subunits. Each subunit has an active site and there is
a ligand in each active site.
After solvating the protein and performing energy
minimization I tried to equilibrate the box by
performing PR MD. but after 100 steps I got LINCS
warning and job crashed.
I switched off pressure coupling and performed PR MD
for 30 and 50 ps but as soon as I turned the pressure
coupling ON I got LINCS warning and again job crashed.
I tried another method ,
I switched off the pressure and performed MD (without
imposing PR)at 50K and raised the temperature by 50
degree every 30 ps up to 300K. But again after
coupling pressure  I faced the same problem.
I have already performed MD for monomers ( subunit A,
B , C, D) and all possible dimers and trimer (AB , AC,
AD,...,ABC ,ABD ,...). The MD went on perfectly
So I can assume there is not any bad contacts.
what can be the reason for LINCS warning and how I can
solve the problem?
Thanking in advance.

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