[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

Dear colleagues,

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:

        #include "popc.itp"

Also, to the bottom of the file (if missing):

; Include position restraint file
#ifdef POSRES
#include "posre.itp"

; Include water topology
#ifdef FLEX_SPC
#include "flexspc.itp"
#include "spc.itp"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000

[ system ]
; Name
Protein in POPC

[ molecules ]
; Compound        #mols
Protein             1
POPC                114
SOL                 2460

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 
double precision.
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 
for MD.

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.

Best regards,

Martina Bertsch, Ph.D.
Northwestern University
Feinberg School of Medicine
Molecular Pharmacology and Biological Chemistry
303 East Chicago Avenue
Chicago, IL 60611

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