[gmx-users] LINCS warning: "Relative constraint deviation after LINCS"
Martina Bertsch, PhD
mbe404 at lulu.it.northwestern.edu
Tue Nov 11 21:05:01 CET 2003
I am simulating a GPC receptor embedded in a POPC membrane. According to
the protocol described in share/tutor/make_hole, I have generated the
protein accessible surface with GRASP, created a hole with a 1.2 nm
radius and run mdrun modified by Smith and Tieleman with hfm 25 and a
2-fs step for 20 ps.
Next, I create the GPCR_popc.pdb by merging the mdrun_make_hole output
and the GPCR.pdb and convert the merged file into gro format. I create
the GPCR_popc.top by including the following lines in the GPCR.top:
After #include "ffgmx.itp" I add:
Also, to the bottom of the file (if missing):
; Include position restraint file
; Include water topology
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
[ system ]
Protein in POPC
[ molecules ]
; Compound #mols
Next, I attempt to run an EM with the following GPCR_popc_em.mdp file:
title = MT1_popc25 EM to settle waters prior to PR-MD
cpp = /lib/cpp
define = -DFLEX_SPC
constraints = none
integrator = steep
nsteps = 10000
nstlist = 10
ns_type = grid
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.2
; Energy minimizing stuff
emtol = 100.0
emstep = 0.001
After ~40 steps I get an error message:
"Stepsize too small (... nm). Converged to machine precision, but
not to the requested precision (...)"
Searching the gmx archive, I find that this is because the SD algorithm
has problems and that the CG may give better results if you compile in
However, if the only aim is to start a MD simulation, then SD is good
enough and the final conformation from the EM can be used as an input
So, I use the final structure from my EM run as an input for the PR-MD.
My GPCR_popc_pr.mdp is attached below.
When I try running mdrun, I get a LINCS warning:
"Relative constraint deviation after LINCS"
and the simulation stops at step 0.
How can I modify my *pr.mdp to remedy this?
Your advice is appreciated.
Martina Bertsch, Ph.D.
Feinberg School of Medicine
Molecular Pharmacology and Biological Chemistry
303 East Chicago Avenue
Chicago, IL 60611
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